A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray.

The origins, design, fabrication and performance of an Atlantic salmon microarray are described. The microarray comprises 16 950 Atlantic salmon-derived cDNA features, printed in duplicate and mostly sourced from pre-existing expressed sequence tag (EST) collections [SALGENE and salmon genome project (SGP)] but also supplemented with cDNAs from suppression subtractive hybridization libraries and candidate genes involved in immune response, protein catabolism, lipid metabolism and the parr-smolt transformation. A preliminary analysis of a dietary lipid experiment identified a number of genes known to be involved in lipid metabolism. Significant fold change differences (as low as 1.2x) were apparent from the microarray analysis and were confirmed by quantitative real-time polymerase chain reaction analysis. The study also highlighted the potential for obtaining artefactual expression patterns as a result of cross-hybridization of similar transcripts. Examination of the robustness and sensitivity of the experimental design employed demonstrated the greater importance of biological replication over technical (dye flip) replication for identification of a limited number of key genes in the studied system. The TRAITS (TRanscriptome Analysis of Important Traits of Salmon)-salmon genome project microarray has been proven, in a number of studies, to be a powerful tool for the study of key traits of Atlantic salmon biology. It is now available for use by researchers in the wider scientific community.

Interferon type I and type II responses in an Atlantic salmon (Salmo salar) SHK-1 cell line by the salmon TRAITS/SGP microarray.

Interferons (IFNs) are cytokines that have proinflammatory, antiviral, and immunomodulatory effects and play a central role during a host response to pathogens. The IFN family contains both type I and type II molecules. While there are a number of type I IFNs, there is only one type II IFN. Recently both type I and type II IFN genes have been cloned in salmonid fish and recombinant proteins produced showing IFN activity. We have stimulated an Atlantic salmon cell line (SHK-1) with both type I and type II recombinant salmonid IFNs and analyzed the transcriptional response by microarray analysis. Cells were exposed to recombinant IFNs for 6 or 24 h or left unexposed as controls. RNA was hybridized to an Atlantic salmon cDNA microarray (salmon 17K feature TRAITS/SGP array) in order to assess differential gene expression in response to IFN exposure. For IFN I and II, 47 and 72 genes were stimulated, respectively; most genes were stimulated by a single IFN type, but some were affected by both IFNs, indicating coregulation of the IFN response in fish. Real-time PCR analysis was employed to confirm the microarray results for selected differentially expressed genes in both a cell line and primary leukocyte cultures.

Transcriptome response following administration of a live bacterial vaccine in Atlantic salmon (Salmo salar).

Antibacterial responses have been studied in Atlantic salmon following an acute intra peritoneal injection of a genetically attenuated (aroA(-)) strain of Aeromonas salmonicida known to elicit protective immunity. Three tissues were studied for transcriptional changes, the liver, head kidney and the gill. RNA was collected from fish 6, 12, 24 and 48 h following infection or at the same time points from fish injected with PBS as non-infected control. PCR-select cDNA subtraction libraries were constructed from pooled 24 and 48 h post infection RNA to identify up-regulated mRNAs. One thousand four hundred and eighty six cDNA clones were sequenced from enriched cDNA libraries, of which 71% had significant homologies to known functional proteins. Many of these clones have previously been un-characterised in Atlantic salmon. A salmonid cDNA microarray was used to further analyse the gene expression profile as the library construction in itself does not answer the dynamics of the response. The greatest increase in expression identified in the array analysis was a liver antibacterial peptide, hepcidin that was increased 11-fold following the challenge. A panel of clones were chosen for semiquantitative reverse transcriptase PCR from all time points sampled. These results indicated there were both temporal differences and tissue differences in the transcriptional response to bacterial exposure, potentially of relevance to the establishment of protection.

Proteomic sensitivity to dietary manipulations in rainbow trout.

Changes in dietary protein sources due to substitution of fish meal by other protein sources can have metabolic consequences in farmed fish. A proteomics approach was used to study the protein profiles of livers of rainbow trout that have been fed two diets containing different proportions of plant ingredients. Both diets control (C) and soy (S) contained fish meal and plant ingredients and synthetic amino acids, but diet S had a greater proportion of soybean meal. A feeding trial was performed for 12 weeks at the end of which, growth and protein metabolism parameters were measured. Protein growth rates were not different in fish fed different diets; however, protein consumption and protein synthesis rates were higher in the fish fed the diet S. Fish fed diet S had lower efficiency of retention of synthesised protein. Ammonia excretion was increased as well as the activities of hepatic glutamate dehydrogenase and aspartate amino transferase (ASAT). No differences were found in free amino acid pools in either liver or muscle between diets. Protein extraction followed by high-resolution two-dimensional electrophoresis, coupled with gel image analysis, allowed identification and expression of hundreds of protein. Individual proteins of interest were then subjected to further analysis leading to protein identification by trypsin digest fingerprinting. During this study, approximately 800 liver proteins were analysed for expression pattern, of which 33 were found to be differentially expressed between diets C and S. Seventeen proteins were positively identified after database searching. Proteins were identified from diverse metabolic pathways, demonstrating the complex nature of gene expression responses to dietary manipulation revealed by proteomic characterisation.

Protein synthesis costs could account for the tissue-specific effects of sub-lethal copper on protein synthesis in rainbow trout (Oncorhynchus mykiss).

This study investigates protein synthesis, following exposure to sub-lethal Cu, in rainbow trout in vivo and in vitro. The investigation has two aims: to determine if perturbations in protein synthesis, compared with other physiological changes, are a biomarker of Cu pollution and to evaluate the most productive role of cellular models in ecotoxicology. Protein synthesis rates were measured by labelling with 3H-phenylalanine. In vivo this was applied by a single (i.p.) injection and in vitro by bathing the cells in 3H-phenylalanine labelled culture media. The effects in vivo were tissue specific. After 3 weeks' exposure to 0.7 microM Cu only skin protein synthesis was reduced. Gills and liver from the same fish were unaffected. This reduction in skin protein synthesis appears to be more sensitive than some other biomarkers reported in the literature. However, Cu concentrations greater by orders of magnitude were required to reproduce this reduction in protein synthesis in skin cell explants (200 and 400 microM). Hepatocyte protein synthesis was unaffected by 10, 20 and 40 microM Cu and a separate investigation has also shown that 25 and 75 microM Cu does not effect protein synthesis in cultured gill cells. Oxygen consumption rates were also measured in vitro by monitoring the decline in O2 partial pressure. The Cu concentrations given above resulted in a decline in O2 consumption rates in the respective cell types. By measuring protein synthesis and O2 consumption after treatment with a protein synthesis inhibitor (cycloheximide), the costs of protein synthesis were also determined. Synthesis costs in hepatocytes are close to the theoretical minimum and are only marginally affected by Cu. Gill cell synthesis costs are also minimal and are unaffected. In skin explants, the reduction in protein synthesis was accompanied by greatly increased synthesis costs. This in vitro result offers a hypothesis as to the tissue-specific effects in vivo; i.e. the energetic demand of protein synthesis may determine tissue sensitivity or susceptibility. Cell or tissue types with high protein synthesis rates are able to avoid detrimental increases in the synthesis cost when exposed to Cu. In tissues with a low protein synthesis rate any further reduction is more likely to incur a potentially damaging increase in protein synthesis costs. Thus, whilst in vitro models may have little practical use in environmental monitoring, they may be best used as a mechanistic tool in understanding susceptibility or tolerance to sub-lethal Cu.

Effects of salmon lice Lepeophtheirus salmonis on sea trout Salmo trutta at different times after seawater transfer.

The physiological and behavioural effects and skin damage caused by salmon lice Lepeophtheirus salmonis (Krøyer) infections on sea trout Salmo trutta L. smolts were greater in fish infected with lice 2 wk after seawater transfer than in fish infected 6 wk after seawater transfer. The initial prevalence of infection was 100% for both groups and the intensity of infection decreased significantly with time over 5 wk. Significantly fewer of the fish infected 2 wk after seawater transfer had resumed feeding by the end of the experiment, leading to a loss of body condition. Furthermore, these fish suffered more severe damage to the skin and detrimental changes in physiological integrity than fish infected 6 wk after seawater transfer as a direct consequence of feeding preadult lice, leading to osmoregulatory failure and death. Although this study was carried out in laboratory conditions, results indicate that lice infections may potentially have a detrimental impact on the survival of wild smolts after seawater transfer.

Changes in physiological parameters and feeding behaviour of Atlantic salmon Salmo salar infected with sea lice Lepeophtheirus salmonis.

Atlantic salmon Salmo salar L. artificially infected with salmon lice Lepeophtheirus salmonis (Krøyer 1837) recovered from detrimental physiological changes and skin damage induced by preadult lice as the parasites matured. Growth rates of Atlantic salmon remained unaffected by lice infection, but food consumption decreased with increasing feeding and movement of the lice prior to and post-mating, correlating with the appearance of head erosions and detrimental changes in physiological integrity. Food consumption of the fish increased as the lice moulted to the adult stage and gravid female lice settled in a posterior location on the fish, subsequently reducing the impact of infection and allowing recovery of the skin damage. However, the impact of preadults was limited, as the decrease in food consumption of fish at 21 d post-infection had no effect on either the specific growth rate or condition factor of the fish. Furthermore, the intensity of lice infections at each of the sample days was not correlated with food consumption, specific growth rate or any of the haematological or physiological parameters measured, either before or after infection, indicating that lice intensity was independent of social dominance/subordinance. This work has provided the first evidence that infected fish can recover from the detrimental changes caused by lice infection, even when they are still infected with lice. If fish can survive the preadult stage of lice, then the mortal impact of lice infections is greatly reduced.

Feed efficiency of rainbow trout can be improved through selection: different genetic potential on alternative diets.

To assess the genetic potential for selection of increased feed efficiency in rainbow trout (Oncorhynchus mykiss), we estimated the heritabilities and correlations for BW, daily weight gain (DG), and daily feed intake (DFI). Body weight was recorded 5 times, and DG and DFI 3 times during a feeding trial lasting 22 mo. To test the hypothesis that phenotypic and genetic parameters were influenced by a nutritional environment, fish were fed either a modern normal protein diet (NP, 40 to 45% protein and 30 to 33% lipid) or an alternative high protein diet (HP, 50 to 56% protein, 20 to 24% lipid) in a split-family design. Results showed that there were no large differences in heritabilities between the diets. Average heritability for DFI over both diets and different fish ages was low (average h2 = 0.10), indicating that modest genetic changes in response to selection can be obtained. Average heritabilities for BW and DG over both diets and different fish ages were 0.28 and 0.33, respectively. The NP diet enabled fish to express a wide range of BW, as shown by the increased coefficients of phenotypic variation for BW. Fish fed the HP diet showed increased phenotypic variation for DFI in > 750-g fish. On the NP diet, genetic correlations of DFI with DG and BW were very strong for 750- to 2,000-g fish. In contrast, on the HP diet, the respective correlations were moderate to low, revealing more genetic potential to change growth and feed intake simultaneously in opposite directions. An analysis of the predicted selection responses showed that selection solely for high DG improved feed efficiency as a correlated genetic response. Simultaneous selection for high DG and reduced DFI, in turn, may increase genetic gain in feed efficiency by a factor of 1.2 compared with selection solely for DG. However, variation for growth and feed intake and the relationships between these traits were different in different nutritional environments, leading to divergent genetic responses on the alternative diets.

The energetic cost of protein synthesis in isolated hepatocytes of rainbow trout (Oncorhynchus mykiss).

To establish the energetic cost of protein synthesis, isolated trout hepatocytes were used to measure protein synthesis and respiration simultaneously at a variety of temperatures. The presence of bovine serum albumin was essential for the viability of isolated hepatocytes during isolation, but, in order to measure protein synthesis rates, oxygen consumption rates and RNA-to-protein ratios, BSA had to be washed from the cells. Isolated hepatocytes were found to be capable of protein synthesis and oxygen consumption at constant rates over a wide range of oxygen tension. Cycloheximide was used to inhibit protein synthesis. Isolated hepatocytes used on average 79.7 +/- 9.5% of their total oxygen consumption on cycloheximide-sensitive protein synthesis and 2.8 +/- 2.8% on maintaining ouabain-sensitive Na+/K(+)-ATPase activity. The energetic cost of protein synthesis in terms of moles of adenosine triphosphate per gram of protein synthesis decreased with increasing rates of protein synthesis at higher temperatures. It is suggested that the energetic cost consists of a fixed (independent of synthesis rate) and a variable component (dependent on synthesis rate).

Protein synthesis in trout liver is stimulated by both feeding and fasting.

The response of protein synthesis in the liver of the rainbow trout to feeding and fasting was investigated in 3 experiments. In the first experiment, the fractional rate of protein synthesis (k s ), %/day) appeared to cycle with daily feeding events being increased by 46%, 123%, and 72% at 1.5h, 3h, and 6h, after a meal. In Experiment 2, liver protein synthesis fell progressively with fasting to a basal level at 4d which was only 20% of the value at 3h after feeding. Liver weight (hepatosomatic index, HSI, % body weight), total RNA and total protein also fell gradually. Between 4d and 6d, both the RNA/protein ratio and the rate of protein synthesis were significantly increased (11% and 74%). At this time, however, there was also a large loss of liver protein suggesting a concomitant increase in protein breakdown. In the last experiment, when trout were pre-fed a low ration (0.6%/d for 2 wks, LR group), the HSI and liver total RNA and protein were largely unaffected by the 6d fast (i.e., relative to the body weight). In this group, however, protein synthesis at 3h was significantly higher than in fish pre-fed a high ration (1.5%/d, HR group). In addition, at 6d after feeding, protein synthesis had increased back to fed levels in the LR group only. It is concluded that protein synthesis in the liver of the trout is influenced both by feeding events and by ration size and also by the degree to which the trout is fasted.

Gill protein turnover: costs of adaptation.

Measurements of gill protein synthesis, and hence turnover, were greatly facilitated over the last decade by the application of "flooding dose" methodology to non-mammalian species. Numerous studies show that in fish and aquatic invertebrates, gills are among the most active tissues with respect to protein turnover, this being true under a variety of environmental and nutritional conditions. The main components being turned over in fish gills are probably collagen, primarily in the gill arches, and epithelial cell proteins in the filaments, both arches and filaments having similar protein synthesis rates. Intriguingly, differences are apparent between protein synthesis rates of adjacent holobranchs, the first (most anterior) being significantly more active than the second or third, perhaps hinting at functional differences between holobranchs. Experimental estimates of energetic costs for protein synthesis, derived from cycloheximide treatment of isolated perfused gills, give a maximum value of 14 mmol O2/g protein synthesized, which is about double theoretical costs. Environmental stressors, such as heavy metals or acid/aluminum, have variable effects on branchial protein turnover. Limited data suggest that zinc or acid exposure depresses protein synthesis, whereas acid/aluminum increases it quite markedly. Calculations indicate that whereas effects within the gills may be substantial, in terms of whole animal energetics, the costs of branchial adaptation are likely to be small.

The effect of short-term fasting and a single meal on protein synthesis and oxygen consumption in cod, Gadus morhua.

Rates of protein synthesis and oxygen consumption (MO2) in cod were compared in both fasted and refed animals. During a 14-day fast both protein synthesis and respiration rates fell to stable values after 6 days. When a meal of whole sandeel at 6% body weight was fed to fish fasted for 6 days, protein synthesis and MO2 increased to a maximum at between 12 and 18 h after feeding. Peak MO2 was about twice the pre-feeding values, while whole animal protein synthesis increased four-fold. There were differences between tissues in the timing of maximum protein synthesis; the liver and stomach responded faster than the remainder of the body. Maximum protein synthesis rates in the liver and stomach occurred at 6 h after feeding, at which time their calculated contribution to total MO2 was 11%. Similar calculations suggested that the integrated increment in whole animal protein synthesis contributed between 23% and 44% of the post-prandial increase in MO2. It was concluded that protein synthesis is an important contributor to increased MO2 after feeding in cod.

Feed consumption, growth and growth efficiency of rainbow trout (Oncorhynchus mykiss (Walbaum)) fed on diets containing a bacterial single-cell protein.

The aim of the present study was to compare the nutritive value of bacterial single-cell protein (BSCP) with that of fishmeal in rainbow trout (Oncorhynchus mykiss (Walbaum)). Four diets were formulated to contain a total of 458 g crude protein/kg of which 0% was from BSCP in diet 1 (BSCP-0), 25% in diet 2 (BSCP-25), 62.5% in diet 3 (BSCP-62.5) and 100% in diet 4 (BSCP-100); the remainder of the protein was from fishmeal. There were two studies: in study 1, duplicate groups of twenty-five fish were fed on one of the four experimental diets at the rate of 20 g/kg body weight per d for 132 d. Feed consumption rates of individual fish were measured using radiography and the overall apparent absorption efficiency for N in each group was measured over a 2-week period. In study 2, N intake, consumption, absorption and accretion were measured for each fish under controlled environmental conditions (12 h: 12 h light-dark regime; 14 degrees). Higher dietary levels of BSCP resulted in significantly higher feed consumption rates but reduced N absorption efficiency and growth rates. However, a diet containing 25% BSCP (75% fishmeal) did not significantly influence growth rates, feed consumption and absorption efficiency compared with a 100% fishmeal diet. The N growth efficiencies were highest in fish fed on the diet containing the highest level of fishmeal and significantly decreased with increasing BSCP content. Construction of N budgets demonstrated that the reduction in growth in fish eating an increasingly larger proportion of BSCP was due to a decrease in N absorption and an increase in the excretion of urea.

RNA turnover and protein synthesis in fish cells.

Protein synthesis in fish has been previously correlated with RNA content. The present study investigates whether protein and RNA synthesis rates are similarly related. Protein and RNA synthesis rates were determined from 3H-phenylalanine and 3H-uridine incorporation, respectively, and expressed as % x day(-1) and half-lives, respectively. Three fibroblast cell lines were used: BF-2, RTP, CHSE 214, which are derived from the bluegill, rainbow trout and Chinook salmon, respectively. These cells contained similar RNA concentrations (approximately 175 microg RNA x mg(-1) cell protein). Therefore differences in protein synthesis rates, BF-2 (31.3 +/- 1.8)>RTP (25.1 +/- 1.7)>CHSE 214 (17.6 +/-1.1), were attributable to RNA translational efficiency. The most translationally efficient RNA (BF-2 cells), 1.8 mg protein synthesised x microg(-1) RNA x day(-1), corresponded to the lowest RNA half-life, 75.4 +/- 6.4 h. Translationally efficient RNA was also energetically efficient with BF-2 cells exploiting the least costly route of nucleotide supply (i.e. exogenous salvage) 3.5-6.0 times more than the least translationally efficient RNA (CHSE 214 cells). These data suggest that differential nucleotide supply, between intracellular synthesis and exogenous salvage, constitutes the area of pre-translational flexibility exploited to maintain RNA synthesis as a fixed energetic cost component of protein synthesis.

Changes in tissue and plasma free amino acid concentrations after feeding in Atlantic cod.

Atlantic cod, Gadus morhua, were maintained on a diet of sandeel and after a 6-day fast were refed a single meal. Concentrations of free amino acids (AAs) were measured in hepatic portal and cardiac blood as well as in the stomach and white muscle at intervals of 6h up to 24h post-feeding. The appearance of both essential and non-essential AAs in the hepatic portal blood was significantly correlated, up to 12h after feeding, to their abundance in the diet. There was a significant decline in total AA concentration in cardiac blood after 6h, followed by a significant increase at 12h. No significant changes in total AA concentration were observed in the other tissues, although mean concentration increased at 12 or 18h. At a more detailed level, the post-prandial changes in concentration of some essential AAs were consistent with their having a role in the stimulation of protein synthesis after feeding.

Growth, feeding frequency, protein turnover, and amino acid metabolism in European lobster Homarus gammarus L.

The effect of feeding frequency on growth and protein metabolism in the European lobster, Homarus gammarus, was investigated. Fourth (IV) stage lobsters H. gammarus were fed individually a marine animal meal (herring/mussels meal) for 56 days. Feeding a daily ration equivalent to 10% of their body weight gave better growth than feeding daily rations of 5% and 20%. Protein synthesis rates were similar for the three food rations but protein growth rates were significantly lower and protein degradation rates highest in the 5% body weight per day ration group. The efficiency with which synthesised protein was retained as growth was found to be 38% in the in the 10% ratio group. Protein synthesis rates of lobsters were found to be lower than those for shrimps (Penaeus vannamei). The amino acid flux also suggests a lower protein conversion efficiency than shrimps P. vannamei. The results suggests that lobsters are slow, periodic feeders and that growth can be readily increased by manipulation of particular environmental factors such as feeding frequency.

Protein synthesis in a fish heart: responses to increased power output.

The effects of exercise on the rates of protein synthesis in the chambers of the trout heart were investigated in vitro and in vivo. An in vitro rainbow trout heart preparation was developed which permitted perfusion of the coronary supply to the compact region of the ventricular muscle. This preparation was used to examine the mechanical responses to preload pressures, the oxygen consumption at different power outputs and the rates of protein synthesis in the various heart components. By increasing preload pressure it was possible to double cardiac output, oxygen consumption and power output without changing heart rate. Mechanical efficiency of the hearts was approximately 20%. Perfusion of the coronary vessels improved cardiac output. Protein synthesis was measured in isolated hearts by the incorporation of [3H]phenylalanine added at high concentration (1.35 mmol l-1) to the perfusion medium. The various chambers of the heart showed marked differences in their rates of protein synthesis. Increasing cardiac output and power output in vitro by twofold over 20 min increased the fractional rate of protein synthesis by approximately 2.5-fold in the atrium and ventricle but did not affect the rates in the bulbus arteriosus. Perfusion of the coronary vessels significantly increased the rates of protein synthesis of the compact layer of the ventricle. In vivo there were no significant differences in the fractional protein synthesis rates between the atrium and ventricle; slow-speed continuous swimming over 40 min (1.5 body lengths s-1) caused an increase in the rates of protein synthesis in all the chambers except the bulbus arteriosus. The stimulation in the fractional rates of protein synthesis by approximately 32% was not as great as in vitro. Both in vivo and in vitro the increased rates of protein synthesis occurred without any change in RNA to protein ratios, indicating an improved activity of protein synthesis per unit of RNA. It is concluded that short-term increases in cardiac contractility, possibly acting through the mechanical stretch on the cardiac muscle, stimulated protein synthesis, particularly in the ventricle, through increased ribosomal activity.

Ubiquitin-proteasome-dependent proteolysis in rainbow trout (Oncorhynchus mykiss): effect of food deprivation.

The ubiquitin-proteasome proteolytic pathway is a major route of protein degradation and of particular importance in muscle proteolysis in mammals. In this study, the beta proteasome subunit N3 and polyubiquitin genes of the rainbow trout, Oncorhynchus mykiss, were sequenced and tissue distribution of gene expression was examined. The effects of 14-day food withdrawal were assessed on the N3 subunit and polyubiquitin gene expression in terms of mRNA, 20S proteasome proteolytic activity and ubiquitin protein abundance in trout liver and muscle. Both sequences are highly conserved, and the rainbow trout ubiquitin amino acid sequence is identical to the mammalian protein. The proteasome beta subunit N3 has 92% similarity to the Xenopus sequence. Starvation halved the polyubiquitin mRNA level in liver but had no effect on muscle levels. No significant effect of food withdrawal was observed on the proteasome mRNA in liver or muscle. Food withdrawal decreased the 20S proteasome proteolytic activity and the abundance of ubiquitin protein in both muscle and liver. Co-regulation of the proteasome and ubiquitin was indicated by the high correlation ( R=0.924) between 20S activity and ubiquitin abundance. Overall, this study demonstrates that starvation down-regulates the ubiquitin-proteasome pathway, possibly highlighting differences in the regulation of protein turnover in poikilothermic and endothermic animals.