Lateral line deformities in wild and farmed sea bass (Dicentrarchus labrax,L.) and sea bream (Sparus aurata,L.)

The lateral line of aquaculture fishes has rarely been studied although it is a very important anatomical organ that could serve as an inexpensive and easy tool to distinguish farmed from wild individuals. In the present study, lateral line deformities were examined in both wild and farmed sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata) specimens to try to detail all possible differences between them. In order to do so, the morphology of the trunk lateral line in wild and farmed adults was examined whereby two major deformities were observed in both species: the ‘scale pocket’ deformity (14–40% incidence in all groups) where the specialized scales are missing but the canal underneath is present and the scale print is obvious, and the ‘somatic scales’ deformity (14–56% incidence in farmed individuals only) where the missing lateral line is covered with normal somatic scales. Histological examination confirmed the macroscopic observations in that the lateral line mechanism was present – although damaged – beneath the scale pocket deformity and completely absent beneath the somatic scales deformity. It is argued that the scale pocket deformity is a result of an accident during the life of the fish whereas the somatic scales deformity is an actual deformity in development.     

Red mark syndrome in rainbow trout Oncorhynchus mykiss: Investigation of immune responses in lesions using histology,immunohistochemistry and analysis of immune gene expression

Red mark syndrome (RMS) is an economically significant disease which affects farmed rainbow trout in the United Kingdom, in the US and in mainland Europe. From the pattern of incidence, it appears to be transmissable, although no causative agent has yet been identified. RMS presents as a severe lymphocytic infiltration centred on the dermis and an alternative, host-focused approach was taken to understand the disease through investigating immune responses occurring in the lesion. Lesion and non-lesion skin at different stages of lesion development were examined using histochemistry and immunohistochemistry on paraffin sections. Expression of immune-related genes was compared between lesion and non-lesion skin. Investigation of early stage lesions suggested that the initial immune response is targeted at the region of the scale pocket, with lymphocyte infiltration and anti-tumour necrosis factor (TNF)-α staining of the stratum spongiosum, and increased numbers of major histocompatibility complex (MHC) II-positive cells immediately adjacent to the scale pocket. Gene expression analysis suggested a counterbalancing T helper (Th)1 and T regulatory (Treg) – type response is occurring in the lesion, with repression of Th2 and Th17-type responses.     

Temporal stability of sea louse Lepeophtheirus salmonis Krøyer populations on Atlantic salmon Salmo salar L. of wild, farm and hybrid parentage

Atlantic salmon salmo salar smolts of wild, hybrid and farmed parentage were individually tagged then reared in a sea cage for 8 months. The fish were sampled three times during this period. On all occasions, farmed Atlantic salmon displayed the highest abundance and density of sea lice Lepeophtheirus salmonis , whilst no significant differences were observed between hybrid and wild Atlantic salmon. Percentage variation between the lowest and highest infected groups was as high as 175 and 144% for L. salmonis abundance and density respectively (sample 2). The temporal stability of interindividual sea lice infection levels was investigated pair‐wise between samples using correlation (sample 1 v . 2, 1 v . 3 and 2 v . 3). When calculated using sea louse abundance, correlations ranged from r ² = 0·11, P  < 0·01 to r ² = 0·39, P  < 0·001, but, when the effects of fish size were controlled for by converting abundance to density, all correlations were <  r ² = 0·1. Therefore, these data indicate that a fish's relative infection level in one sample was a weak predictor of its relative infection level in another sample. This suggests that identification of individual Atlantic salmon that display reduced susceptibility to sea lice, may be problematic.     

Crystallographically mapped ligand binding differs in high and low IgE binding isoforms of birch pollen allergen bet v 1

The ability of pathogenesis-related proteins of family 10 to bind a broad spectrum of ligands is considered to play a key role for their physiological and pathological functions. In particular, Bet v 1, an archetypical allergen from birch pollen, is described as a highly promiscuous ligand acceptor. However, the detailed recognition mechanisms, including specificity factors discriminating binding properties of naturally occurring Bet v 1 variants, are poorly understood.Here, we report crystal structures of Bet v 1 variants in complex with an array of ligands at a resolution of up to 1.2 Å. Residue 30 within the hydrophobic pocket not only discriminates in high and low IgE binding Bet v 1 isoforms but also induces a drastic change in the binding mode of the model ligand deoxycholate. Ternary crystal structure complexes of Bet v 1 with several ligands together with the fluorogenic reporter 1-anilino-8-naphthalene sulfonate explain anomalous fluorescence binding curves obtained from 1-anilino-8-naphthalene sulfonate displacement assays. The structures reveal key interaction residues such as Tyr83 and rationalize both the binding specificity and promiscuity of the so-called hydrophobic pocket in Bet v 1.The intermolecular interactions of Bet v 1 reveal an unexpected complexity that will be indispensable to fully understand its roles within the physiological and allergenic context.     

Inhibitory effects of alcohols on the activity of human matrix metalloproteinase 7 (matrilysin)

Aliphatic alcohols inhibited the activity of human matrix metalloproteinase 7 (matrilysin) competitively with K(i) of 6.1-19.4% (v/v) or 0.66-4.80 M. From the relationship between the structures of alcohols and their K(i) values, alcohols are considered to bind the hydrophobic S1' subsite most plausibly, and the size of the pocket was estimated to be large enough to accommodate the length of 1-butanol (4-carbon chain) and the bulk of tertiary alcohols. Alcohols might be suitable probes for exploring the active-site geometry of enzymes.     

SSU rRNA gene sequence reveals two genotypes of Spironucleus barkhanus (Diplomonadida) from farmed and wild Arctic charr Salvelinus alpinus

Spironucleus barkhanus isolated from the blood of Arctic charr Salvelinus alpinus from a marine fish farm were genetically compared with S. barkhanus isolated from the gall bladder of wild Arctic charr. The wild Arctic charr were caught in the lake used as the water source for the hatchery from which the farmed fish originated. Sequencing of the small subunit ribosomal RNA gene (SSU rDNA) from these 2 populations showed that the isolates obtained from farmed and wild Arctic charr were only 92.7 % similar. Based on the sequence differences between these isolates, it is concluded that the parasites isolated from the farmed fish have not been transmitted from wild Arctic charr in the hatchery's fresh water source. It is therefore most likely that the farmed fish were infected by S. barkhanus after they were transferred to seawater. S. barkhanus isolated from diseased farmed Arctic charr were 99.7% similar to the isolates obtained from diseased farmed Chinook (Canada) and Atlantic salmon (Norway). The high degree of sequence similarity between S. barkhanus from farmed Arctic charr, Chinook and Atlantic salmon indicates that systemic spironucleosis may be caused by specific strains/variants of this parasite. The genetic differences between the isolates of farmed and wild fish are of such magnitude that their conspecificity should be questioned.     

Novel X-ray sequences and crystal structures of Persian and Starry sturgeon methemoglobins: Highlighting the role of heme pocket waters in causing autoxidation

Although there is a high sequence similarity between mammalian and fish hemoglobin (Hb), the oxidation and heme loss rates can vary greatly between them such that fish Hbs oxidise much more rapidly than mammalian Hbs. There is to date no sequence or structural data for any sturgeon Hb to reveal the level of autoxidation in these fish. In this study, novel high resolution X-ray sequences and crystal structures of methemoglobin (Met-Hb) from two sturgeon fish including Persian sturgeon (Acipenser percisus) and Starry sturgeon (Acipenser stellatus) belonging to the Caspian sea has been determined. A comprehensive sequence and structure comparison between these sturgeon Met-Hbs and a number of non-sturgeon and normal and sickle cell anaemia human Hb in varying heme states has been carried out highlighting (i) the structural variability in the heme propionate groups; (ii) the existence of certain residues or their displacement and shift in the heme pocket allowing entry of water molecules into the heme pocket; (iii) the importance of the number of water molecules in the heme pocket; (iv) the hydrogen bonding between oxygens of A and D propionate groups and that of waters in the heme pocket; and (v) the role of heme binding waters causing oxidative stress and heme autoxidation.     

Ligand binding channels reflected in the resonance Raman spectra of cryogenically trapped species of myoglobin

Variations in the v2 region of the Raman spectra of cryogenically trapped photoproducts of different liganded myoglobins as a function of ligand (CO, O2, and n-butyl isocyanide) and species (whale, tuna, elephant) are reported. These variations are attributed to differences in the population of "open" (ligand accessible) and "closed" (ligand inaccessible) conformations of the distal heme pocket. Based on these findings and those derived from other spectroscopies including x-ray crystallography, NMR, IR spectra, and ESR, a working model is presented which accounts for how the conformation of the distal heme pocket, the geometry of the bound ligand, the identity of the ligand, and the dynamics of the dissociated ligand are all interconnected.     

Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules

We determined the crystal structure of the motor domain of the fast fungal kinesin from Neurospora crassa (NcKin). The structure has several unique features. (i) Loop 11 in the switch 2 region is ordered and enables one to describe the complete nucleotide-binding pocket, including three inter-switch salt bridges between switch 1 and 2. (ii) Loop 9 in the switch 1 region bends outwards, making the nucleotide-binding pocket very wide. The displacement in switch 1 resembles that of the G-protein ras complexed with its guanosine nucleotide exchange factor. (iii) Loop 5 in the entrance to the nucleotide-binding pocket is remarkably long and interacts with the ribose of ATP. (iv) The linker and neck region is not well defined, indicating that it is mobile. (v) Image reconstructions of ice-embedded microtubules decorated with NcKin show that it interacts with several tubulin subunits, including a central beta-tubulin monomer and the two flanking alpha-tubulin monomers within the microtubule protofilament. Comparison of NcKin with other kinesins, myosin and G-proteins suggests that the rate-limiting step of ADP release is accelerated in the fungal kinesin and accounts for the unusually high velocity and ATPase activity.     

Resonance Raman studies of iron spin and axial coordination in distal pocket mutants of ferric myoglobin

We have used resonance Raman spectroscopy to study 11 distal pocket mutants and the "wild type" and native ferric sperm whale myoglobin. The characteristic Raman core-size markers v4, v3, v2, and v10 are utilized to assign the spin and coordination state of each sample. It is demonstrated that replacements of the distal and proximal histidines can discriminate against H2O as a sixth ligand and favor a pentacoordinate Fe3+ atom. Soret absorption band blueshifts are correlated with the pentacoordinate heme environment. One E7 replacement (Arg) leads to an iron spin state change and produces a low spin species. The Glu and Ala mutations at position E11 leave the protein's spin and coordination unaltered. A laser-induced photoreduction effect is observed in all pentacoordinate mutants and seems to be correlated with the loss of the heme-bound water molecule.     

Migratory behaviour of wild and farmed Atlantic salmon (Salmo salar) during spawning

Migratory behaviour at spawning of wild and newly-escaped farmed Atlantic salmon was analysed by radio telemetry in the River Alta, North Norway. Spawning areas were located by aerial surveys. Farmed females moved significantly more than wild females ( P <0.01). There was no such difference between the two groups of males. About 83% of the wild fish stayed within identified spawning areas for 1 day or longer. The corresponding figure for farmed salmon was only 43% ( P <0.05). Wild salmon stayed 8.1 days inside spawning areas and farmed salmon 5.2 days. The present results suggest that escaped farmed salmon had reduced spawning success compared with wild fish.     

Experimental infection of rainbow trout Oncorhynchus mykiss with viral haemorrhagic septicaemia virus isolates from European marine and farmed fishes

The susceptibility of rainbow trout Oncorhynchus mykiss to infection with various isolates of viral haemorrhagic septicaemia virus (VHSV) was examined. A total of 8 experiments with rainbow trout ranging from 0.6 to 6.2 g was conducted for 139 isolates originating from wild marine fishes in European waters (115 isolates), farmed turbot from Scotland and Ireland (2 isolates), and farmed rainbow trout (22 isolates). The isolates were tested by immersion and/or intraperitoneal injection either as pooled or single isolates. The isolates from wild marine fishes did not cause mortality by immersion while some of the isolates caused mortality when injected. All VHSV isolates from farmed rainbow trout caused significant mortality by immersion. Currently, pathogenicity trials are the only way to differentiate VHSV isolates from wild marine fishes and farmed rainbow trout. The 2 farmed turbot isolates did not cause mortality by immersion, supporting the view that they originated from the marine environment.     

Can variation in standard metabolic rate explain context‐dependent performance of farmed Atlantic salmon offspring?

Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild‐type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self‐maintenance) during domestication. Fitness‐related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g., social dominance) depend on environmental conditions, such as food availability. We hypothesize that farmed offspring have an advantage at high food availability due to, for example, dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy‐demanding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed‐wild hybrids and pure wild offspring. Next, we test early‐life performance (in terms of survival and growth) of hybrids relative to that of their wild half‐siblings, as well as their competitive abilities, in semi‐natural conditions of high and low food availability. Finally, we test how SMR affects early‐life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi‐natural streams. Yet, the presence of hybrids led to decreased survival of their wild half‐siblings. Contrary to our hypothesis about context‐dependency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon.     

Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip

Genetic interactions between farmed and wild conspecifics are of special concern in fisheries where large numbers of domesticated individuals are released into the wild. In the Atlantic salmon (Salmo salar), selective breeding since the 1970's has resulted in rapid genetic changes in commercially important traits, such as a doubling of the growth rate. Each year, farmed salmon escape from net pens, enter rivers, and interbreed with wild salmon. Field experiments demonstrate that genetic introgression may weaken the viability of recipient populations. However, due to the lack of diagnostic genetic markers, little is known about actual rates of gene flow from farmed to wild populations. Here we present a panel of 60 single nucleotide polymorphisms (SNPs) that collectively are diagnostic in identifying individual salmon as being farmed or wild, regardless of their populations of origin. These were sourced from a pool of 7000 SNPs comparing historical wild and farmed salmon populations, and were distributed on all but two of the 29 chromosomes. We suggest that the generic differences between farmed and wild salmon at these SNPs have arisen due to domestication. The identified panel of SNPs will permit quantification of gene flow from farmed to wild salmon populations, elucidating one of the most controversial potential impacts of aquaculture. With increasing global interest in aquaculture and increasing pressure on wild populations, results from our study have implications for a wide range of species.     

Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees

In some wild Atlantic salmon populations, rapid declines in numbers of wild returning adults has been associated with an increase in the prevalence of farmed salmon. Studies of phenotypic variation have shown that interbreeding between farmed and wild salmon may lead to loss of local adaptation. Yet, few studies have attempted to assess the impact of interbreeding at the genome level, especially among North American populations. Here, we document temporal changes in the genetic makeup of the severely threatened Magaguadavic River salmon population (Bay of Fundy, Canada), a population that might have been impacted by interbreeding with farmed salmon for nearly 20 years. Wild and farmed individuals caught entering the river from 1980 to 2005 were genotyped at 112 single-nucleotide polymorphisms (SNPs), and/or eight microsatellite loci, to scan for potential shifts in adaptive genetic variation. No significant temporal change in microsatellite-based estimates of allele richness or gene diversity was detected in the wild population, despite its precipitous decline in numbers over the last two decades. This might reflect the effect of introgression from farmed salmon, which was corroborated by temporal change in linkage-disequilibrium. Moreover, SNP genome scans identified a temporal decrease in candidate loci potentially under directional selection. Of particular interest was a SNP previously shown to be strongly associated with an important quantitative trait locus for parr mark number, which retained its genetic distinctiveness between farmed and wild fish longer than other outliers. Overall, these results indicate that farmed escapees have introgressed with wild Magaguadavic salmon resulting in significant alteration of the genetic integrity of the native population, including possible loss of adaptation to wild conditions.     

Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study

Turbot Scophthalmus maximus is the focus of a rapidly expanding aquaculture industry, while at the same time wild catches appear to be in decline. As a preliminary investigation into the effects of hatchery rearing, genetic variation at three polymorphic microsatellite loci was assessed in two wild populations and two farmed strains of turbot, from Ireland and Norway. Although a considerable loss of rare alleles was observed in the Irish farmed strain, no statistically significant reductions were found in mean heterozygosity or allelic diversity in farmed strains compared to wild populations. Significant genetic heterogeneity was found between wild and farmed samples from each country but not between the two wild populations. Genetic differentiation between the farmed strains was presumed to be caused by drift in the hatcheries. The utility of these particular microsatellite loci in comparing these samples and the importance of molecular genetic testing of farmed strains is stressed.     

Comparison of fatty acids and some mineral matter profiles of wild and farmed snails,Cornu aspersum Müller, 1774

ABSTRACT

The fatty acid and mineral matter compositions of the visceral mass and pedal mass of wild and farmed Cornu aspersum were compared. The relative fatty acid amounts of the visceral and pedal masses of wild and farmed snails are: polyunsaturated fatty acid (PUFA) > saturated fatty acid (SFA) > monounsaturated fatty acid (MUFA), PUFA?>?SFA?>?MUFA, MUFA?>?PUFA?>?SFA and PUFA?>?MUFA?>?SFA, respectively. Wild snails had a higher concentration of iron and zinc than farmed snails. Selenium was 2.82 times higher in the pedal mass of farmed snails than the pedal mass of wild snails. Ca:P ratios in the visceral mass of wild snails, visceral mass and pedal mass of farmed snails were 1.76:1, 1.12:1 and 3.87:1 respectively. Both wild and farmed snails have high contents of oleic, linoleic, eicosapentaenoic and docosahexaenoic fatty acids and are a good source of minerals. Careful attention should be paid, however, as to which diet will be used during farming because the composition of fatty acid in the snail is affected by diet.     

Development and characterization of ten novel microsatellite loci for the emu (Dromaius novaehollandiae) and genetic diversity of Japanese farm populations

Molecular Biology Reports - The emu (Dromaius novaehollandiae) is a useful poultry animal farmed for fat, meat, and eggs. Genetic structure and relationships among farmed emu populations in Japan...