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Work was supported by the Natural Environment Research Council (NE/I014632/1 to M.G.R., A.R.C., and R.R.S), the Natural Environment Research Council Biomolecular Analysis Facility (NBAF654 to M.G.R), and the Swedish Research Council (Vetenskapsrådet; 2018-04598 to R.R.S). Postcopulatory interactions between the sexes in internally fertilizing species elicits both sexual conflict and sexual selection. Macroevolutionary and comparative studies have linked these processes to rapid transcriptomic evolution in sex-specific tissues and substantial transcriptomic postmating responses in females, patterns of which are altered when mating between reproductively isolated species. Here we test multiple predictions arising from sexual selection and conflict theory about the evolution of sex-specific and tissue-specific gene expression and the postmating response at the microevolutionary level. Following over 150 generations of experimental evolution under either reduced (enforced monogamy) or elevated (polyandry) sexual selection in Drosophila pseudoobscura, we found a substantial effect of sexual selection treatment on transcriptomic divergence in virgin male and female reproductive tissues (testes, male accessory glands, the female reproductive tract and ovaries). Sexual selection treatment also had a dominant effect on the postmating response, particularly in the female reproductive tract ? the main arena for sexual conflict - compared to ovaries. This effect was asymmetric with monandry females typically showing more postmating responses than polyandry females, with enriched gene functions varying across treatments. The evolutionary history of the male partner had a larger effect on the postmating response of monandry females, but females from both sexual selection treatments showed unique patterns of gene expression and gene function when mating with males from the alternate treatment. Our microevolutionary results mostly confirm comparative macroevolutionary predictions on the role of sexual selection on transcriptomic divergence and altered gene regulation arising from divergent coevolutionary trajectories between sexual selection treatments. Publisher PDF

The state of an animal prior to the application of a noxious stimulus can have a profound effect on their nociceptive threshold and subsequent behaviour. In mammals, the presence of acute stress preceding a painful event can have an analgesic effect whereas the presence of chronic stress can result in hyperalgesia. While considerable research has been conducted on the ability of stress to modulate mammalian responses to pain, relatively little is known about fish. This is of particular concern given that zebrafish (Danio rerio) are an extensively used model organism subject to a wide array of invasive procedures where the level of stress prior to experimentation could pose a major confounding factor. This study, therefore, investigated the impact of both acute and chronic stress on the behaviour of zebrafish subjected to a potentially painful laboratory procedure, the fin clip. In stress-free individuals, those subjected to the fin clip spent more time in the bottom of the tank, had reduced swimming speeds and less complex swimming trajectories; however, these behavioural changes were absent in fin-clipped fish that were first subject to either chronic or acute stress, suggesting the possibility of stress-induced analgesia (SIA). To test this, the opioid antagonist naloxone was administered to fish prior to the application of both the stress and fin-clip procedure. After naloxone, acutely stressed fin-clipped zebrafish exhibited the same behaviours as stress-free fin-clipped fish. This indicates the presence of SIA and the importance of opioid signalling in this mechanism. As stress reduced nociceptive responses in zebrafish, this demonstrates the potential for an endogenous analgesic system akin to the mammalian system. Future studies should delineate the neurobiological basis of stress-induced analgesia in fish., Summary: Exposure of zebrafish to acute or chronic stress prior to fin clipping prevents behavioural changes normally seen after fin clip; naloxone treatment prevented this effect, demonstrating stress-induced analgesia.

Fish production is increasingly important to global food security. A major factor in maintaining health, productivity and welfare of farmed fish is the establishment and promotion of a stable and beneficial intestinal microbiota. Understanding the effects of factors such as host and environment on gut microbial community structure is essential for developing strategies for stimulating the establishment of a health-promoting gut-microbiota. We compared intestinal microbiota of common carp and rainbow trout, two fish with different dietary habits, sourced from various farm locations. There were distinct differences in the gut microbiota of carp and trout intestine. The microbiota of carp was dominated by Fusobacteriia and Gammaproteobacteria, while the trout microbiota consisted predominantly of Mollicutes and Betaproteobacteria. The majority of bacterial sequences clustered into a relatively low number of operational taxonomic units (OTUs) revealing a comparatively simple microbiota, with Cetobacterium, Aeromonas and Mycoplasma being highly abundant. Within each species, fish from different facilities were found to have markedly similar predominant bacterial populations despite distinctly different rearing environments, demonstrating intra-species uniformity and significant influence of host selectivity. This study demonstrates that in fish the host species imparts substantial impact in shaping the community structure of the intestinal microbiota.

Fish are used in a variety of experimental contexts often in high numbers. To maintain their welfare and ensure valid results during invasive procedures it is vital that we can detect subtle changes in behaviour that may allow us to intervene to provide pain-relief. Therefore, an automated method, the Fish Behaviour Index (FBI), was devised and used for testing the impact of laboratory procedures and efficacy of analgesic drugs in the model species, the zebrafish. Cameras with tracking software were used to visually track and quantify female zebrafish behaviour in real time after a number of laboratory procedures including fin clipping, PIT tagging, and nociceptor excitation via injection of acetic acid subcutaneously. The FBI was derived from activity and distance swum measured before and after these procedures compared with control and sham groups. Further, the efficacy of a range of drugs with analgesic properties to identify efficacy of these agents was explored. Lidocaine (5 mg/L), flunixin (8 mg/L) and morphine (48 mg/L) prevented the associated reduction in activity and distance swum after fin clipping. From an ethical perspective, the FBI represents a significant refinement in the use of zebrafish and could be adopted across a wide range of biological disciplines.

The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population, and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. When compared against the N2 reference, the CB4856 genome has 327,050 single nucleotide variants (SNVs) and 79,529 insertion–deletion events that result in a total of 3.3 Mb of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 but not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, which have a greatly elevated SNV density, ranging from 2 to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors, suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.

BackgroundCryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population.ResultsWe measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40-57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL.ConclusionsThese results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 hours) and that CGV is mainly determined by response related trans regulatory eQTL.

The ability to assess welfare is an important refinement that will ensure the good condition of animals used in experimentation. The present study investigated the impact of invasive procedures on the patterns of movement of zebrafish (Danio rerio). Recordings were made before and after fin clipping, PIT tagging and a standard pain test and these were compared with control and sham handled zebrafish. The fractal dimension (FD) from the 3D trajectories was calculated to determine the effect of these treatments on the complexity of movement patterns. While the FD of zebrafish trajectories did not differ over time in either the control or sham group, the FDs of the treatment groups reduced in complexity. The FD of fish injected with different strengths of acetic acid declined in a dose-dependent manner allowing us to develop an arbitrary scale of severity of the treatments. The 3D trajectory plots from some groups indicated the presence of repetitive swimming patterns akin to stereotypical movements. When administered with lidocaine, which has analgesic properties, the movement complexity of fin clipped fish reverted to a pattern that resembled that of control fish. Fractal analysis of zebrafish locomotion could potentially be adopted as a tool for fish welfare assessment.

Chill and freeze represent very different components of low temperature stress. Whilst the principal mechanisms of tissue damage and of acquired protection from freeze-induced effects are reasonably well established, those for chill damage and protection are not. Non-freeze cold exposure (i.e. chill) can lead to serious disruption to normal life processes, including disruption to energy metabolism, loss of membrane perm-selectivity and collapse of ion gradients, as well as loss of neuromuscular coordination. If the primary lesions are not relieved then the progressive functional debilitation can lead to death. Thus, identifying the underpinning molecular lesions can point to the means of building resistance to subsequent chill exposures. Researchers have focused on four specific lesions: (i) failure of neuromuscular coordination, (ii) perturbation of bio-membrane structure and adaptations due to altered lipid composition, (iii) protein unfolding, which might be mitigated by the induced expression of compatible osmolytes acting as ‘chemical chaperones’, (iv) or the induced expression of protein chaperones along with the suppression of general protein synthesis. Progress in all these potential mechanisms has been ongoing but not substantial, due in part to an over-reliance on straightforward correlative approaches. Also, few studies have intervened by adoption of single gene ablation, which provides much more direct and compelling evidence for the role of specific genes, and thus processes, in adaptive phenotypes. Another difficulty is the existence of multiple mechanisms, which often act together, thus resulting in compensatory responses to gene manipulations, which may potentially mask disruptive effects on the chill tolerance phenotype. Consequently, there is little direct evidence of the underpinning regulatory mechanisms leading to induced resistance to chill injury. Here, we review recent advances mainly in lower vertebrates and in arthropods, but increasingly in genetic model species from a broader range of taxa.

Ecological speciation occurs with the adaptation of populations to different environments and concurrent evolution of reproductive isolation. Phenotypic plasticity might influence both ecological adaptation and reproductive traits. We examined environmentspecific gene expression and male mating success in cactophilic Drosophila mojavensis using transcriptome sequencing. This species exhibits cactus-dependent mating success across different species of host plants, with genotype-by-environment interactions for numerous traits. We cultured flies from egg to eclosion on two natural cactus hosts and surveyed gene expression in adult males that were either successful or unsuccessful in achieving copulation in courtship trials. We identified gene expression differences that included functions involved with metabolism, most likely related to chemical differences between host cactus species. Several epigenetic-related functions were identified that might play a role in modulating gene expression in adults due to host cactus effects on larvae, and mating success. Cactus-dependent mating success involved expression differences of genes implicated in translation, transcription, and nervous system development. This suggests a role of neurological function genes in the mating success of D. mojavensis males. Together, these results suggest that the influence of environmental variation on mating success via regulation of gene expression might be an important aspect of ecological speciation.

Nearly all aptamers identified so far for any given target molecule have been specific for the same binding site (epitope). The most notable exception to the 1 aptamer per target molecule rule is the pair of DNA aptamers that bind to different epitopes of thrombin. This communication refutes the suggestion that these aptamers exist because different partitioning methods were used when they were selected. The possibility that selection of these aptamers was biased by conflicting secondary structures was also investigated and found not to contribute. The preparation of protein-coated magnetic beads for systematic evolution of ligands by exponential enrichment (SELEX) and the different specificities of the thrombin aptamers for the α and β forms of thrombin are also reported.

Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one of the most clearcut ecological examples of anthropogenically induced ED in aquatic ecosystems. To identify the underpinning mechanisms of imposex for this 'nonmodel' species, we combined Roche 454 pyrosequencing with custom oligoarray fabrication inexpensively to both generate gene models and identify those responding to chronic tributyltin (TBT) treatment. The results supported the involvement of steroid, neuroendocrine peptide hormone dysfunction and retinoid mechanisms, but suggested additionally the involvement of putative peroxisome proliferator-activated receptor (PPAR) pathways. Application of rosiglitazone, a well-known vertebrate PPARγ ligand, to dogwhelks induced imposex in the absence of TBT. Thus, while TBT-induced imposex is linked to the induction of many genes and has a complex phenotype, it is likely also to be driven by PPAR-responsive pathways, hitherto not described in invertebrates. Our findings provide further evidence for a common signalling pathway between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption. The authors would like to thank Prof. Neil Hall, Dr Margaret Hughes and Dr Delphine Lallias for technical advice. We also acknowledge the long-term support of NERC at both Bangor and Liverpool. This work was supported by Fundação para a Ciência e a Tecnologia (FCT) Ph.D. grant SFRH/BD/27711/ 2006 awarded to Sonia Pascoal and by Natural Environment Research Council Molecular Genetics Facility (NERC MGF) grant 294 awarded to Simon Creer. published

Current aquatic chemical testing guidelines recognize that solvents can potentially interfere with the organism or environmental conditions of aquatic ecotoxicity tests and therefore recommend concentration limits for their use. These recommendations are based on evidence of adverse solvent effects in apical level tests. The growing importance of subapical and chronic endpoints in future test strategies, however, suggests that the limits may need reassessment. To address this concern, microarrays were used to determine the effects of organic solvents, dimethylformamide (DMF) and dimethylsulfoxide (DMSO), on the transcriptome of zebrafish (Danio rerio) embryos. Embryos were exposed for 48 h to a range of concentrations between 0.025 and 32.0 ml/L. Effects on survival and development after 24 and 48 h were assessed microscopically, with no effects on mortality or morphology up to 2.0 and 16.0 ml/L for DMF and DMSO. However, analysis of 48-h embryonic RNA revealed large numbers of differentially expressed genes at concentrations well below the 0.1 ml/L solvent limit level. The enrichment of differentially expressed genes was found for metabolic, developmental, and other key biological processes, some of which could be linked to observed morphological effects at higher solvent concentrations. These findings emphasize the need to remove or lower as far as possible the concentrations of solvent carriers in ecotoxicology tests.

In 2000, fishermen reported the appearance of deformed reproductive organs in whitefish (Coregonus spp.) from Lake Thun, Switzerland. Despite intensive investigations, the causes of these abnormalities remain unknown. Using gene expression profiling, we sought to identify candidate genes and physiological processes possibly associated with the observed gonadal deformations, in order to gain insights into potential causes. Using in situ-synthesized oligonucleotide arrays, we compared the expression levels at 21,492 unique transcript probes in liver and head kidney tissue of male whitefish with deformed and normally developed gonads, respectively. The fish had been collected on spawning sites of two genetically distinct whitefish forms of Lake Thun. We contrasted the gene expression profiles of 56 individuals, i.e., 14 individuals of each phenotype and of each population. Gene-by-gene analysis revealed weak expression differences between normal and deformed fish, and only one gene, ictacalcin, was found to be up-regulated in head kidney tissue of deformed fish from both whitefish forms, However, this difference could not be confirmed with quantitative real-time qPCR. Enrichment analysis on the level of physiological processes revealed (i) the involvement of immune response genes in both tissues, particularly those linked to complement activation in the liver, (ii) proteolysis in the liver and (iii) GTPase activity and Ras protein signal transduction in the head kidney. In comparison with current literature, this gene expression pattern signals a chronic autoimmune disease in the testes. Based on the recent observations that gonad deformations are induced through feeding of zooplankton from Lake Thun we hypothesize that a xenobiotic accumulated in whitefish via the plankton triggering autoimmunity as the likely cause of gonad deformations. We propose several experimental strategies to verify or reject this hypothesis.

An understanding of the underpinning physiology and biochemistry of animals is essential to properly understand the impact of anthropogenic changes and natural catastrophes upon the conservation of endangered species. An observation on the tissue location of the key respiratory protein, myoglobin, now opens up new opportunities for understanding how hypoxia tolerance impacts on diving lifestyle in turtles. The respiratory protein, myoglobin has functions other than oxygen binding which are involved in hypoxia tolerance, including metabolism of reactive oxygen species and of the vascular function by metabolism of nitric oxide. Our work aims to determine whether myoglobin expression in the green turtle exists in multiple non muscle tissues and to confirm the hypothesis that reptiles also have a distributed myoglobin expression which is linked to the hypoxiatolerant trait. This initial work in turtle hatch Chelonia mydas confirms the presence of myoglobin transcriptin brain, heart and liver tissues. Furthermore, it will serve as a tool for completing the sequence and generating an in situ hybridization probe for verifying of cell location in expressing tissues .

Sesamin enhances the DHA content of tissue lipids in salmonid fish. We have examined whether this effect also occurs in common carp (Cyprinus carpio). Two-year-old common carps were fed a diet containing 5.8 g sesamin kg−1 feed for 69 days. No significant differences were found in the fish weight, specific growth rate, food conversion ratio and lipid content in white muscle. The experimental diet with sesamin increased the percentage of 18:3 n-3 and decreased 18:4 n-3, 22:5 n-3, 22:6 n-3 as well as the desaturation index reflecting the ratio of n-3 long-chain polyunsaturated fatty acids/18:3 n-3 in the triacylglycerol fraction. Sesamin increased the total cytochrome P450 content in hepatopancreatic microsomes as well as 7-ethoxyresorufin O-deethylase (EROD) activity. However, a detailed microarray analysis using 26K gene probes failed to establish any significant pattern of transcriptional response, including lipid biosynthetic genes. Together, these results indicate that under conditions of our study, sesamin was ineffective in the common carp as a means of achieving the changes in the tissue lipid composition as were seen in salmonids.

The Van Gogh-like 2 (vangl2) gene is typically associated with planar cell polarity pathways, which is essential for correct orientation of epithelial cells during development. The encoded protein of this gene is a transmembrane protein and is highly conserved through evolution. Van Gogh-like 2 was selected for further study on the basis of consistent regulation after a nociceptive stimulus in adult common carp and rainbow trout in a microarray study. An in situ hybridisation was conducted in the brain of mature common carp (Cyprinus carpio), 1.5 and 3 h after a nociceptive stimulus comprising of an acetic acid injection to the lips of the fish and compared with a saline-injected control. The vangl2 gene was expressed in all brain regions, and particularly intensely in neurons of the telencephalon and in ependymal cells. In the cerebellum, a greater number (P=0.018) of Purkinje cells expressed vangl2 after nociception (n=7) compared with controls (n=5). This regulation opens the possibility that vangl2 is involved in nociceptive processing in the adult fish brain and may be a novel target for central nociception in vertebrates.

SUMMARY Myoglobin (Mb) is famous as a muscle-specific protein – yet the common carp expresses the gene (cMb1) encoding this protein in a range of non-muscle tissues and also expresses a novel isoform (cMb2)in the brain. Using a homologous antibody and riboprobes, we have established the relative amounts and cellular sites of non-muscle Mb expression in different tissues. The amounts of carp myoglobin (cMb) in supernatants of different tissues were just 0.4–0.7% relative to that of heart supernatants and were upregulated by two-to-four fold in liver, gill and brain following 5 days of hypoxic treatment. Brain exhibited both cMb proteins in western analysis, whereas all other tissues had only cMb1. We have also identified cells expressing cMb protein and cMb mRNA using immunohistology and RNA in situ hybridisation (RNA-ISH),respectively. Mb was strongly expressed throughout all cardiac myocytes and a subset of skeletal muscle fibres, whereas it was restricted to a small range of specific cell types in each of the non-muscle tissues. These include pillar and epithelial cells in secondary gill lamellae, hepatocytes, some neurones,and tubular epithelial cells in the kidney. Capillaries and small blood vessels in all tissues exhibited Mb expression within vascular endothelial cells. The cMb2 riboprobe located expression to a subset of neurones but not to endothelial cells. In zebrafish, which possesses only one Mb gene, a similar expression pattern of Mb protein and mRNA was observed. This establishes a surprisingly cell-specific distribution of Mb within non-muscle tissues in both carp and zebrafish, where it probably plays an important role in the regulation of microvascular, renal and brain function.

We investigated the effects of fluoxetine, a selective serotonin reuptake inhibitor, on neuroendocrine function and the reproductive axis in female goldfish. Fish were given intraperitoneal injections of fluoxetine twice a week for 14 days, resulting in five injections of 5 μg fluoxetine/g body wt. We measured the monoamine neurotransmitters serotonin, dopamine, and norepinephrine in addition to their metabolites with HPLC. Homovanillic acid, a metabolite in the dopaminergic pathway, increased significantly in the hypothalamus. Plasma estradiol levels were measured by radioimmunoassay and were significantly reduced approximately threefold after fluoxetine treatment. We found that fluoxetine also significantly reduced the expression of estrogen receptor (ER)β1 mRNA by 4-fold in both the hypothalamus and the telencephalon and ERα mRNA by 1.7-fold in the telencephalon. Fluoxetine had no effect on the expression of ERβ2 mRNA in the hypothalamus or telencephalon. Microarray analysis identified isotocin, a neuropeptide that stimulates reproductive behavior in fish, as a candidate gene affected by fluoxetine treatment. Real-time RT-PCR verified that isotocin mRNA was downregulated approximately sixfold in the hypothalamus and fivefold in the telencephalon. Intraperitoneal injection of isotocin (1 μg/g) increased plasma estradiol, providing a potential link between changes in isotocin gene expression and decreased circulating estrogen in fluoxetine-injected fish. Our results reveal targets of serotonergic modulation in the neuroendocrine brain and indicate that fluoxetine has the potential to affect sex hormones and modulate genes involved in reproductive function and behavior in the brain of female goldfish. We discuss these findings in the context of endocrine disruption because fluoxetine has been detected in the environment.

Stearoyl-CoA desaturases (SCDs) are key enzymes of fatty acid biosynthesis whose regulation underpins responses to dietary, thermal, and hormonal treatment. Although two isoforms are known to exist in the common carp and human and four in mouse, there is no coherent view on how this gene family evolved to generate functionally diverse members. Here we identify numerous new SCD homologs in teleost fishes, using sequence data from expressed sequence tag (EST) and cDNA collections and genomic model species. Phylogenetic analyses of the deduced coding sequences produced only partially resolved molecular trees. The multiple SCD isoforms were, however, consistent with having arisen by an ancient gene duplication event in teleost fishes together with a more recent duplication in the tetraploid carp and possibly also salmonid lineages. Critical support for this interpretation comes from comparison across all vertebrate groups of the gene order in the genomic environments of the SCD isoforms. Using syntenically aligned chromosomal fragments from large-insert clones of common carp and grass carp together with those from genomically sequenced model species, we show that the ancient and modern SCD duplication events in the carp lineage were each associated with large chromosomal segment duplications, both possibly linked to whole genome duplications. By contrast, the four mouse isoforms likely arose by tandem duplications. Each duplication in the carp lineage gave rise to differentially expressed SCD isoforms, either induced by cold or diet as previously shown for the recent duplicated carp isoforms or tissue specific as demonstrated here for the ancient duplicate zebrafish isoforms.

The common carp is an important fish species satisfying ornamental, food and recreational fisheries’ needs worldwide, but in common with other cyprinid fishes, it is particularly renowned for its environmental tolerance. Investigating the mechanistic basis of growth, disease and environmental tolerance is greatly enhanced by access to a comprehensive list of gene sequences and post-genomic technologies. The current status of genomic resources is described for this species including 40 k cDNA clone collections, their associated expressed sequence tags (ESTs) and a developing series of 13 k–26 k cDNA microarrays fabricated from amplicons. The arrays have been directed at questions of response to environmental stress (cold and hypoxia), viral and bacterial disease and ectoparasite infection. Consequently, clones from a wide range of tissues were prepared. The authors discuss how these resources were generated and their application. Evidence is presented supporting that the carp microarray may also be useful as a heterologous set of probes in studies of other fish species.

The breadth of mechanistic analyses of environmental stress responses is greatly enhanced by the use of contemporary post-genomic screening technologies, notably including massively parallel transcript analysis by microarray. These genome-wide investigations are entirely dependent upon the creation of a suite of resources that are directed against the species under investigation. Here, the authors describe the use of in silico techniques for the filtering of large-scale EST data sets for the rainbow trout, Oncorhynchus mykiss, down to a non-redundant collection of c. 21 500 BLAST-identified sequences. The authors describe simple optimization procedures to compare the performance of different oligonucleotide probes predicted to hybridize to each of the trout sequences, so that the best performing probe could be selected. The collection of optimized probes was then submitted to a commercial oligoarray fabrication platform and the arrays used for specific experiments. This design approach leverages publicly available sequence data, thereby dramatically reducing production costs. Given an ability to incorporate additional sequence data, and inexpensively commissioning the updated oligoarray designs, this offers a highly cost-effective route to array experiments even for non-model species. The authors have validated this new microarray by investigating the in vitro responses of cultured rainbow trout cells following anoxia exposure for up to 24 h. The array displays a dynamic range of 104, which greatly exceeds that for cDNA probes, and offers improved consistency between arrays. The authors define 57 genes displaying significant responses and interpret the genes identified within the context of responses to oxygen deprivation.

The life cycle of the European eel (Anguilla anguilla) includes two long migratory periods, when the newly hatched leptocephali larvae drift on ocean currents from the Sargasso Sea to the shores of Western Europe and then again up to 30 years later when adult eels swim back to their place of birth for reproductive purposes. Prior to the migration from fresh water (FW) to sea water (SW) adult yellow eels undergo various anatomical and physiological adaptations (silvering) which promote sexual development and aid the transition to increased environmental salinities. The aim of this study was to identify and characterise changes in gene expression within the major osmoregulatory tissues of the eel which enable these fish to make the physiological adaptations required for transfer to SW environments. In particular, changes in the expression of the FW-adapting hormone prolactin were correlated with differential expression of known osmoregulatory important genes within the gill, intestine and kidney following the acclimation of eels to SW. Various tissues were sampled from individual fish at selected intervals over a 5-month period following FW/SW transfer and RNA was isolated. Suppressive subtractive hybridization (SSH) was used for enrichment of differentially expressed genes. Microarrays comprising 6144 cDNAs spotted in triplicate, from brain, gill, intestine and kidney libraries (1536 randomly selected clones per tissue library), were hybridized with appropriate targets and analysed. Microarray results were validated using known genes implicated in osmoregulation, such as prolactin, growth hormone, Na, K-ATPase and some unknown genes, the role of which in osmoregulation needs to be elucidated.

Protection of poikilothermic animals from seasonal cold is widely regarded as being causally linked to changes in the unsaturation of membrane phospholipids, yet in animals this proposition remains formally untested. We have now achieved this by the genetic manipulation of lipid biosynthesis of Caenorhabditis elegans independent of temperature. Worms transferred from 25°C to 10°C develop over several days a much-increased tolerance of lethal cold (0°C) and also an increased phospholipid unsaturation, as in higher animal models. Of the three C. elegans Δ9-desaturases, transcript levels of fat-7 only were up-regulated by cold transfer. RNAi suppression of fat-7 caused the induction of fat-5 desaturase, so to control desaturase expression we combined RNAi of fat-7 with a fat-5 knockout. These fat-5 / fat-7 manipulated worms displayed the expected negative linear relationship between lipid saturation and cold tolerance at 0°C, an outcome confirmed by dietary rescue. However, this change in lipid saturation explains just 16% of the observed difference between cold tolerance of animals held at 25°C and 10°C. Thus, although the manipulated lipid saturation affects the tolerable thermal window, and altered Δ9-desaturase expression accounts for cold-induced lipid adjustments, the effect is relatively small and none of the lipid manipulations were sufficient to convert worms between fully cold-sensitive and fully cold-tolerant states. Critically, transfer of 10°C-acclimated worms back to 25°C led to them restoring the usual cold-sensitive phenotype within 24 h despite retaining a lipid profile characteristic of 10°C worms. Other nonlipid mechanisms of acquired cold protection clearly dominate inducible cold tolerance.

After the publication of the article, the authors retrospectively noted that the name of Dr Dawn Jones, a postdoctoral researcher in the laboratory of Professor Christine Gosden, should have been added to the authors' list, whose contribution to the study greatly augmented the exploration of all the RNA products via adoption of the RNASeq (Illumina) methodology. All the existing authors agree to the inclusion of Dr Jones as a co‑author, with the exception of Derek Gardener, who has retired from the Institute and is no longer contactable by e-mail (although we are confident that he would not raise any objection). The correct author list (and affiliations) should therefore have been published as follows: Shiva Seyed Forootan1, Joe M. Butler1, Derek Gardener1, Dawn Jones1, Alison E. Baird1, Andrew Dodson1, Alistair Darby2, John Kenny2, Neil Hall2, Andrew R. Cossins2, Christopher S. Foster1,3 and Christine M. Gosden1 1Molecular Pathology Laboratory, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, Faculty of Health and Life Sciences, University of Liverpool, Royal Liverpool University Hospital, Liverpool L69 3GA; 2Center for Genomic Research, University of Liverpool, Liverpool L69 7ZB; 3HCA International, Pathology Laboratories, London WC1E 6JA, UK. We regret the oversight of having failed to include Dr Dawn Jones as an author on this paper. [the original article was published in the International Journal of Oncology 48: 130-144, 2016; DOI: 10.3892/ijo.2015.3222].

Hibernation is a seasonally entrained and profound phenotypic transition to conserve energy in winter. It involves significant biochemical reprogramming, although our understanding of the underpinning molecular events is fragmentary and selective. We have conducted a large-scale gene expression screen of the golden-mantled ground squirrel, Spermophilus lateralis, to identify transcriptional responses associated specifically with the summer-winter transition and the torpid-arousal transition in winter. We used 112 cDNA microarrays comprising 12,288 probes that cover at least 5,109 genes. In liver, the profiles of torpid and active states in the winter were almost identical, although we identified 102 cDNAs that were differentially expressed between winter and summer, 90% of which were downregulated in the winter states. By contrast, in cardiac tissue, 59 and 115 cDNAs were elevated in interbout arousal and torpor, respectively, relative to the summer active condition, but only 7 were common to both winter states, and during arousal none was downregulated. In brain, 78 cDNAs were found to change in winter, 44 of which were upregulated. Thus transcriptional changes associated with hibernation are qualitatively modest and, since these changes are generally less than twofold, also quantitatively modest. Unbiased Gene Ontology profiling of the transcripts suggests a winter switch to β-oxidation of lipids in liver and heart, a reduction in metabolism of toxic compounds and the urea cycle in liver, and downregulated electron transport in the brain. We identified just one strongly winter-induced transcript common to all tissues, namely an RNA-binding protein, RBM3. This analysis clearly differentiates responses of the principal tissues, identifies a large number of new genes undergoing regulation, and broadens our understanding of affected cellular processes that, in part, account for the winter-adaptive hibernating phenotype.

Microarrays, or gene chips, are transforming the way that gene expression is measured by allowing us to determine the expression of thousands of genes from a sample. This gives immense power to examine gene expression on a global scale within individual animals and between animals. The scope for analysing complex animal functions at the molecular level is within our grasp. Relatively few studies have examined complex behaviours and correlated them with gene expression in the central nervous system. Here, we review the use of microarray technology in the dissection of behaviour and focus specifically on dominance status. A cDNA library using suppression subtraction hybridisation on rainbow trout Oncorhynchus mykiss of differing status has been produced to enrich the cDNA library for genes that are differentially expressed between individuals of different dominance status. A preliminary analysis demonstrated that there were 1,165 genes that differed between fish of different dominance status. Therefore, there is the potential of correlating gene expression profile with rank position within dominance hierarchies, thus identifying targets for candidate gene approaches.

We have reconstructed the events that led to the evolution of a key physiological innovation underpinning the large adaptive radiation of fishes, namely their unique ability to secrete molecular oxygen (O 2 ). We show that O 2 secretion into the swimbladder evolved some 100 million years after another O 2 -secreting system in the eye. We unravel the likely sequence in which the functional components of both systems evolved. These components include ocular and swimbladder countercurrent exchangers, the Bohr and Root effects, the buffering power and surface histidine content of hemoglobins, and red blood cell Na + /H + exchange activity. Our synthesis reveals the dynamics of gains and losses of these multiple traits over time, accounting for part of the huge diversity of form and function in living fishes.

The documented 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced effects on zebrafish Danio rerio including craniofacial malformations and a general retardation of growth. were further characterized in the present study. A significant decrease in total body length and the length of each bone in the upper and lower jaw was identified in exposed larvae from an exposure concentration of 30 ng l -1 TCDD. This study is the first quantitative evidence for the effects of TCDD on the upper jaw and also demonstrates that TCDD-induced craniofacial malformations and retardation of growth are very sensitive endpoints of dioxin toxicity.

The beta-adrenergic stress response in red blood cells (RBCs) of rainbow trout shows seasonal changes in expression. We have explored the mechanisms underpinning this response by following, over a period of 27 months, changes in beta-adrenergic receptor (beta-AR) binding characteristics, beta-adrenergically stimulated RBC Na(+)/H(+) exchanger (betaNHE) activity, together with beta-AR and betaNHE mRNA levels and plasma steroid hormone and lactate levels. These parameters were measured at approximately monthly intervals in a single population of fish held under semi-natural conditions. Membrane-bound, high-affinity beta-ARs were present in RBCs at all sampling times, varying from 668+/-112 receptors cell(-1) to 2654+/-882 receptors cell(-1) (mean +/- S.E.M.; N=8). betaNHE activity, however, was reduced by 57% and 34% in December 1999 and February 2001, respectively, compared with an otherwise sustained influx that averaged 110.4+/-2.3 mmol l(-1) RBCs h(-1) (N=119). Only one reduction coincided with a spawning period but both were preceded by transient increases in circulating testosterone. betaNHE activity measured under standard conditions was not correlated with the number or affinity of beta-ARs nor with water temperature, but both beta-AR numbers and betaNHE activity were positively related to their respective mRNA levels (P=0.005 and 0.038, respectively). Pharmaceutical intervention in the transduction cascade linking the beta-AR and betaNHE failed to indicate any failure of the transduction elements in RBCs displaying low betaNHE activity. Similarly, we failed to demonstrate any link between seasonal cortisol fluctuations and seasonally reduced betaNHE activity. However, the betaNHE activity of age-separated RBC fractions showed that younger RBCs had a significantly higher betaNHE response than older RBCs, consistent with the seasonal reductions in betaNHE being linked to turnover of RBCs and erythropoiesis. Testosterone is known to induce erythropoiesis and we conclude that seasonal reductions in betaNHE are not caused by changes in beta-AR numbers but may be linked to testosterone-induced erythropoiesis.

▪ Abstract DNA microarray technology is revolutionizing many aspects of biological research, allowing the expression of many thousands of gene transcripts to be monitored simultaneously. This provides powerful tools for the genome-wide correlation of gene transcript levels with physiological responses and alterations in physiological states. To date, microarray analyses have been applied almost exclusively to a few model species for which the abundant gene sequence data permit the fabrication of whole-genome microarrays. However, many interesting physiological traits and responses are poorly expressed or absent in model species and may be better illustrated in nonmodel organisms. Comparative approaches to understanding function traditionally focus on species that by virtue of their unusual adaptations, lifestyles, and phylogeny are particularly suited to address a specific biological process or problem. In this review, we show that microarray technology can be successfully applied to these nonmodel species and used to generate new insights of comparative and evolutionary significance into animal function.

Fish genomics is developing an increasingly high profile, with the sequencing of four fish genomes (Takifugu, Tetraodon, zebrafish and medaka). However, numerous other fish species are used in laboratories throughout the world (the so-called ‘alternative-model’ or ‘non-model’ fish species), providing unique insights into fields ranging from physiology, toxicology and behaviour to evolution and ecology. The diversity in both species and experimental systems is in many ways both the strength and the weakness of fish as subjects for study. The strength comes from the sheer range of adapted forms and physiologies, many of which offer unique opportunities for exploring fundamental problems in biology. The weakness comes from a rather fragmented fish biology community, which is often species-centric, with collaborations restricted to a limited number of researchers working on the same (or similar) species or, in fewer instances, on the same phenomenon in diverse species. The aim of this discussion workshop was to bring together international fish scientists to review the current use of advanced genomic and post-genomic technologies in diverse fields of fish biology and to foster a new coherence in the coordinated development of screening technologies and the sharing of underpinning resources. This would not only invigorate gene function analysis but also enable new cross-taxon analysis of genome evolution. The workshop was organized by Andrew Cossins (Liverpool, UK) and sponsored by the Natural Environment Research Council (NERC) Environmental Genomics Science Programme and the Biotechnology and Biological Research Council (BBSRC). The invited participants comprised an international mix of US, Japanese and European scientists, with representatives from the major

Carp respond to cold by the upregulated expression of Delta9-acyl-CoA desaturase. Here we report the cloning and characterization of Cds2, a second Delta9-acyl CoA-desaturase expressed in carp liver. Both Cds1 and Cds2 complemented the ole1 mutation in Saccharomyces cerevisiae, permitting the synthesis of delta9-monounsaturates, confirming their identity as delta9-desaturases. We demonstrate that under a standard feeding regime it is the Cds2, and not Cds1, transcript that is transiently upregulated during the first few days of cooling from 30 degrees C to 10 degrees C, the period when cold-induced membrane restructuring occurs. Cds2 exists as two differentially spliced transcripts, differing by a small segment from the 3'-untranslated region, the ratio of which varies with temperature. Feeding a diet enriched in saturated fats produced a fourfold increase in Cds1 transcript levels, which was blocked by cooling to 15 degrees C. Cds2 transcript levels, however, showed no substantial response to the saturated diet. Thus carp liver uniquely expresses two isoforms of delta9-acyl CoA desaturase, possibly formed by a recent duplication event, that are differentially regulated by cooling and dietary treatment.

SUMMARY Cold acclimation of carp from 30°C to 10°C causes a restructuring of liver microsomal phospholipids characterised by increased proportions of monounsaturated fatty acid in phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Here, we have used electrospray ionisation mass spectrometry (ESI-MS) to determine the patterns of alteration to individual molecular species compositions of PC, PE and phosphatidylinositol (PI) in response to gradually decreasing temperature. The results demonstrate that cold induces precise changes to a limited number of phospholipid species, and that these changes are distinct and different for each phospholipid class. The major change for PC was increased 16:1/22:6, but for PE the species that increased was 18:1/22:6. By contrast, the PI species that increased during cold acclimation were characterised by an sn-1 monounsaturated fatty acid in combination with arachidonoyl or eicosapentaenoyl fatty acid at the sn-2 position. Analysis of acyl distribution indicates that cold only caused the accumulation of monounsaturated fatty acids at the sn-1 and not at the sn-2 position of phospholipids. These results highlight the tight and restricted range of modifications that membranes make to their phospholipid composition in response to thermal stress.

Teleost species from cold environments possess more disordered brain synaptic membranes than species from warm habitats, thereby providing equivalent physical structures at their respective habitat temperatures. We have related this adaptive interspecific biophysical response to the fatty acid composition of brain membranes from 17 teleost species obtained from Antarctic, temperate and semi-tropical waters, as well as from rat and turkey as representative homeotherms. Cold-adaptive increases in membrane disorder (determined by fluorescence anisotropy with diphenylhexatriene as probe) were correlated with large and linear increases in the proportion of unsaturated fatty acids, from 35 to 60 % in phosphatidylcholine (PtdCho) and from 55 to 85 % in phosphatidylethanolamine (PtdEth). For PtdCho, the cold-adaptive increase in unsaturation was associated almost entirely with increased proportions (from 7 to 40 %) of polyunsaturated fatty acids (PUFAs), with mono-unsaturates (MUFAs) providing an approximately constant proportion in all species. Exactly opposite effects were evident for phosphatidylethanolamine (PtdEth). Thus, the compositional adaptation for PtdCho occurred largely by exchange of polyunsaturated and mono-unsaturated fatty acid in the sn-2 position, whilst for PtdEth it involved exchanges between saturates and mono-unsaturates at the sn-1 position. This difference may be related to the different molecular shapes of the two phosphoglycerides and the need to maintain the balance between bilayer-stabilising and -destabilising tendencies. This comparative study provides a more comprehensive view of the compositional adjustments that accompany and perhaps account for temperature-adaptive interspecific differences in membrane physical structure.

Larval Dover sole fed an Artemia diet supplemented with n-3 long-chain (C20 + C22) polyunsaturated fatty acids (PUFA) are known to be more resistant to low-temperature injury. Here we explore the relationship between tissue fatty acid composition and tolerance of stressful environmental conditions over the larval and early juvenile periods. Artemia nauplii supplemented with n-3 long-chain PUFA-deficient and PUFA-enriched oil emulsions were fed to two groups of larvae. Whole body tissue samples from the resulting PUFA-deficient and -enriched juveniles possessed 12.1 and 21.9% n-3 long-chain PUFA, respectively. These differences were at the expense of C18 PUFA, while proportions of saturated fatty acids, monounsaturated fatty acids, and total PUFA were unaffected. Brain and eye tissues from the PUFA-deficient fish contained lower levels of 22:6n-3, known to be important for optimal nervous system function, incorporating instead a range of fatty acids of lower unsaturation. PUFA-deprived juveniles showed substantially greater mortality when exposed to a combination of low temperature and low salinity, as well as to high temperature and to hypoxia. After adaptation to the different diets, both dietary groups were fed a common formulated feed high in n-3 long-chain PUFA. Tissue PUFA in both groups progressively increased to the same high value, with a consequent loss of the differences in cold-susceptibility. These correlated changes support a link between dietary manipulation of n-3 long-chain PUFA and development of a stress-sensitive phenotype. PUFA deprivation had no detectable effect upon static hydrocarbon order of purified brain membranes (as assessed by fluorescence polarization) but was associated with an increase in the whole-body content of prostaglandins. We conclude that susceptibility to environmental stress is responsive to dietary n-3 long-chain PUFA manipulation, possibly due to altered tissue development or the overproduction of eicosanoids.

Hypotonic swelling of teleost erythrocytes activates multiple transport systems leading to the regulatory decrease of cell volume. We have examined using pharmacological manipulation the swelling-induced taurine flux pathway in red blood cells of the rainbow trout and its relationship to swelling-induced K flux pathways. We show that the activation and deactivation of taurine flux is rapid and that the flux is a sigmoidal function of cell volume. N-ethylmaleimide (NEM) and the non-specific protein kinase inhibitor, staurosporine, both inactivated the hypotonically-induced taurine flux with concentrations eliciting half-maximal inhibition (IC50s) of 212 and 17 micromol(-1), respectively. The low taurine fluxes under isotonic conditions were unaffected. By contrast, the tyrosine kinase inhibitor, genistein, partially inhibited taurine flux under both isotonic and hypotonic conditions. The specific phosphatase inhibitor, calyculin A, had no inhibitory or stimulatory effect under either condition whilst the less-specific phosphatase inhibitor, ortho-vanadate, reduced taurine flux only under hypotonic conditions. In these respects the regulatory control of the taurine pathway differs from the Cl-dependent K flux. However, NEM and staurosporine also inhibited the Cl-independent K flux, both with similar IC50s to those observed for taurine fluxes. This supports the idea of the hypotonically-induced taurine flux and the Cl-independent K flux sharing the same transport pathway.

Oxygen is essential for all higher forms of animal life. It is required for oxidative phosphorylation, which forms the bulk of the energy supply of most animals. In many vertebrates, transport of O(2) from respiratory to other tissues, and of CO(2) in the opposite direction, involves red cells. These are highly specialised, adapted for their respiratory function. Intracellular haemoglobin, carbonic anhydrase and the membrane anion exchanger (AE1) increase the effective O(2)- and CO(2)-carrying capacity of red cells by approximately 100-fold. O(2) also has a pathological role. It is a very reactive species chemically, and oxidation, free radical generation and peroxide formation can be major hazards. Cells that come into contact with potentially damaging levels of O(2) have a variety of systems to protect them against oxidative damage. Those in red cells include catalase, superoxide dismutase and glutathione. In this review, we focus on a third role of O(2), as a regulator of membrane transport systems, a role with important consequences for the homeostasis of the red cell and also the organism as a whole. We show that regulation of red cell transporters by O(2) is widespread throughout the vertebrate kingdom. The effect of O(2) is selective but involves a wide range of transporters, including inorganic and organic systems, and both electroneutral and conductive pathways. Finally, we discuss what is known about the mechanism of the O(2) effect and comment on its physiological and pathological roles.

Cold acclimation induces a transient enzymatic activation of the acyl CoA-Δ9-desaturase in carp liver. We have determined thresholds for two underlying mechanisms; namely, the activation of latent enzyme and the induced synthesis of new desaturase. Carp were progressively cooled from 30 °C to 23, 17 and 10 °C, where they were held for up to 5 days. Endoplasmic reticulum phospholipids showed substantial changes in fatty acid composition, with linear decreases in the proportion of saturates with temperature over the full range of cooling (11.3 % in phosphatidylcholine and 15.8 % in phosphatidylethanolamine). In the phosphatidyl-ethanolamine fraction, this was linked to increased proportions of monoenes, particularly 20:1(n-9). Modest cooling to 23 °C on day 1 induced a 2.5-fold transient increase in Δ9-desaturase activity without any change in the amount of desaturase protein or transcript. Further cooling to 17 °C induced a greater and more sustained increase in desaturase activity, reaching sevenfold on day 5, with a 10- to 20-fold increase in the amount of desaturase transcript. Extreme cooling to 10 °C led to a very large, but transient, 40- to 50-fold increase in desaturase transcript amounts, a modest 40–50 % increase in desaturase protein but no further increase in activity over that observed at 17 °C. These results distinguish at least three mechanisms involved in cold-induced lipid restructuring; the activation of latent desaturase observed with gentle cooling, the induction of desaturase gene transcription and, finally, a third unidentified lipid compensatory mechanism that occurs with extreme cooling. The complex nature of cold-induced lipid restructuring also involves changes in the activity of other biosynthetic enzymes, including elongase and positional- and phospholipid-specific acyltransferases.

1. Cl--dependent K+ (86Rb+) influxes were measured in oxygenated and deoxygenated equine red blood cells, whose free [Mg2+]i had been clamped, to examine the effect on O2 dependency of the K+-Cl- cotransporter. 2. Total [Mg2+]i was 2.55 +/- 0.07 mM (mean +/- s.e.m. , n = 6). Free [Mg2+]i was estimated at 0.45 +/- 0.04 and 0.68 +/- 0. 03 mM (mean +/- s.e.m., n = 4) in oxygenated and deoxygenated red cells, respectively. 3. K+-Cl- cotransport was minimal in deoxygenated cells but substantial in oxygenated ones. Cl--dependent K+ influx, inhibited by calyculin A, consistent with mediation via the K+-Cl- cotransporter, was revealed by depleting deoxygenated cells of Mg2+. 4. Decreasing [Mg2+]i stimulated K+ influx, and increasing [Mg2+]i inhibited it, in both oxygenated and deoxygenated red cells. When free [Mg2+]i was clamped, Cl--dependent K+ influxes were always greater in oxygenated cells than in deoxygenated ones, and changes in free [Mg2+]i of the magnitude occurring during oxygenation-deoxygenation cycles had a minimal effect. Physiological fluctuations in free [Mg2+]i are unlikely to provide the primary link coupling activity of the K+-Cl- cotransporter with O2 tension. 5. Volume and H+ ion sensitivity of K+ influx in Mg2+-clamped red cells were increased in O2 compared with those in deoxygenated cells at the same free [Mg2+]i, by about 6- and 2-fold, respectively, but again these features were not responsible for the higher fluxes in oxygenated cells. 6. Regulation of the K+-Cl- cotransporter by O2 is very similar in equine, sheep and in normal human (HbA) red cells, but altered in human sickle cells. Present results imply that, as in sheep red cells, O2 dependence of K+-Cl- cotransport in equine red cells is not mediated via changes in free [Mg2+]i and that cotransport in Mg2+-clamped red cells is still stimulated by O2. This behaviour is contrary to that reported for human sickle (HbS) cells.

Organismal development is the most dynamic period of the life cycle, yet we have only a rough understanding of the dynamics of gene expression during adolescent transition. Here we show that adolescence in Caenorhabditis elegans is characterized by a spectacular expression shift of conserved and highly polymorphic genes. Using a high resolution time series we found that in adolescent worms over 10,000 genes changed their expression. These genes were clustered according to their expression patterns. One cluster involved in chromatin remodelling showed a brief up-regulation around 50 h post-hatch. At the same time a spectacular shift in expression was observed. Sequence comparisons for this cluster across many genotypes revealed diversifying selection. Strongly up-regulated genes showed signs of purifying selection in non-coding regions, indicating that adolescence-active genes are constrained on their regulatory properties. Our findings improve our understanding of adolescent transition and help to eliminate experimental artefacts due to incorrect developmental timing.

Holding Your BreathHemoglobin and myoglobin are widely responsible for oxygen transport and storage (see the Perspective byRezende). The ability of diving mammals to obtain enough oxygen to support extended dives and foraging is largely dependent on muscle myoglobin (Mb) content.Mircetaet al.(p.1234192) found that in mammalian lineages with an aquatic or semiaquatic lifestyle, Mb net charge increases, which may represent an adaptation to inhibit self-association of Mb at high intracellular concentrations. Epistasis results from nonadditive genetic interactions and can affect phenotypic evolution.Natarajanet al.(p.1324) found that epistatic interactions were able to explain the increased hemoglobin oxygen-binding affinity observed in deer mice populations at high altitude. In mammals, the offloading of oxygen from hemoglobin is facilitated by a reduction in the blood's pH, driven by metabolically produced CO2. However, in fish, a reduction in blood pH reduces oxygen carrying capacity of hemoglobin.Rummeret al.(p.1327) implanted fiber optic oxygen sensors within the muscles of rainbow trout and found that elevated CO2levels in the water led to acidosis and elevated oxygen tensions.

Cold exposure of carp leads to the induced activity of the hepatic delta 9-desaturase (Schünke, M. and Wodtke, E. (1983) Biochim. Biophys. Acta 734, 70-75). We have investigated the controlled expression of this enzyme using isolated carp hepatocytes. Culture at 30 degrees C, of cells isolated from 30 degrees C-acclimated carp. resulted in an 8-13-fold increase in desaturase-specific activity over 4 days, whilst another enzyme of intermediary metabolism, glucose-6-phosphatase, decreased by more than 60%. This desaturase induction was associated with a loss of intracellular lipid vesicles and with increases in the levels of oleic acid of membrane phosphoglycerides and corresponding decreases in 22:6(n - 3). Supplementation of cultures with oleic acid and with polyunsaturated fatty acids did not cause any reduction in the desaturase induction. The level of immunodetectable desaturase protein increased during culture at 30 degrees C and a desaturase mRNA was detected after 2 days of culture by Northern analysis. These results suggest that in vitro culture leads to an increased synthesis of desaturase protein by means of activated gene transcription. Significantly, transfer of cultures of 30 degrees C-acclimated hepatocytes to 10 degrees C resulted in a smaller induction of desaturase activity; thus cold transfer of cells in itself did not induce hepatocyte desaturase activity as does whole animal cooling. This suggests either that cold induction of desaturase activity in vivo involves systemic control or that the conditions imposed by culture prevent cold induction.

Poikilothermic animals respond to chronic cold by increasing phosphoglyceride unsaturation to restore the fluidity of cold-rigidified membranes. Despite the importance of this compensatory response, the enzymes involved have not been clearly identified, and the mechanisms that control their activity are unknown. In carp liver, cold induces an 8- to 10-fold increase in specific activity of the microsomal stearoyl coenzyme A desaturase. Cold-induced up-regulation of gene transcription resulted in a 10-fold increase in desaturase transcript amounts after 48 to 60 hours. However, this increase was preceded by the activation of latent desaturase, probably by a posttranslational mechanism. These two mechanisms may act sequentially to match desaturase expression to the demands imposed by a progressive decrease in temperature.

Stereological sampling regimes, in particular volume and number estimation, often require systematic uniformly random sections throughout a specimen. A method has been developed to increase the efficiency of preparing fish larvae for sectioning prior to histological or stereological analysis. Embedding a group of larvae in a resin block using this technique greatly reduces the quantity of sections produced and allows easy assessment of sample groups. Saving time in this way therefore makes stereology a more viable research tool.

Because of a recent whole genome duplication, the hypoxia-tolerant common carp and goldfish are the only vertebrates known to possess two myoglobin (Mb) paralogs. One of these, Mb1, occurs in oxidative muscle but also in several other tissues, including capillary endothelial cells, whereas the other, Mb2, is a unique isoform specific to brain neurons. To help understand the functional roles of these diverged isoforms in the tolerance to severe hypoxia in the carp, we have compared their O2 equilibria, carbon monoxide (CO) and O2 binding kinetics, thiol S-nitrosation, nitrite reductase activities, and peroxidase activities. Mb1 has O2 affinity and nitrite reductase activity comparable to most vertebrate muscle Mbs, consistent with established roles for Mbs in O2 storage/delivery and in maintaining nitric oxide (NO) homeostasis during hypoxia. Both Mb1 and Mb2 can be S-nitrosated to similar extent, but without oxygenation-linked allosteric control. When compared with Mb1, Mb2 displays faster O2 and CO kinetics, a lower O2 affinity, and is slower at converting nitrite into NO. Mb2 is therefore unlikely to be primarily involved in either O2 supply to mitochondria or the generation of NO from nitrite during hypoxia. However, Mb2 proved to be significantly faster at eliminating H2O2, a major in vivo reactive oxygen species (ROS), suggesting that this diverged Mb isoform may have a specific protective role against H2O2 in the carp brain. This property might be of particular significance during reoxygenation following extended periods of hypoxia, when production of H2O2 and other ROS is highest.

Theoretical and empirical studies have sought to explain the formation and maintenance of social relationships within groups. The resulting dominance hierarchies have significant fitness and survival consequences dependent upon social status. We hypothesised that each position or rank within a group has a distinctive brain gene expression profile that correlates with behavioural phenotype. Furthermore, transitions in rank position should determine which genes shift in expression concurrent with the new dominance status. We used a custom cDNA microarray to profile brain transcript expression in a model species, the rainbow trout, which forms tractable linear hierarchies. Dominant, subdominant and submissive individuals had distinctive transcript profiles with 110 gene probes identified using conservative statistical analyses. By removing the dominant, we characterised the changes in transcript expression in sub-dominant individuals that became dominant demonstrating that the molecular transition occurred within 48 hours. A strong, novel candidate gene, ependymin, which was highly expressed in both the transcript and protein in subdominants relative to dominants, was tested further. Using antibody injection to inactivate ependymin in pairs of dominant and subdominant zebrafish, the subdominant fish exhibited a substantial increase in aggression in parallel with an enhanced competitive ability. This is the first study to characterise the molecular signatures of dominance status within groups and the first to implicate ependymin in control of aggressive behaviour. It also provides evidence for indirect genetic effect models in which genotype/phenotype of an individual is influenced by conspecific interactions within a group. The variation in the molecular profile of each individual within a group may offer a new explanation of intraspecific variation in gene expression within undefined groups of animals and provides new candidates for empirical study.

Coral bleaching has taken centre-stage in the debate over the likely biological effects of global environmental change. Central to any judgements on this issue is the ability of corals to display increased tolerance of debilitating or lethal conditions through phenotypic adaptations, such as heat-hardening, longer-term acclimatisation responses or even trans-generational epigenetic effects. But the key question is whether the magnitude of such responses can match the predicted increases in sea temperatures over the period of global warming. In the recent literature, much has been said about the potential for acclimatisation in tropical reef corals and how it may, or may not, be significant in the context of the world’s changing climate (Hughes et al. 2003; Hoegh-Guldberg 2004; Donner et al. 2007; Hoegh-Guldberg et al. 2007; Maynard et al. 2008a; Donner 2009). In fact, we know remarkably little about the potential for and extent of acclimatisation in corals, and the complex physiology and behaviour underlying the phenomenon (Edmunds and Gates 2008; Maynard et al. 2008a). It is important at this stage to define the terms used in this chapter following Bligh and Johnson (1973) since there has been, and continues to be, considerable confusion in their use in the literature together with established concepts in thermal biology (see Box 1).

Large-scale toxicogenomic screening approaches offer great promise for generating a bias-free system-wide view of toxicological effects and modes-of-action of chemicals and ecotoxicants. However, early applications of microarray technology have identified relatively small groups of responding genes with which to define new targets for analysis by conventional means. We have trialled a more intensive approach to the design and interpretation of array experiments incorporating a balanced interwoven ANOVA design with higher levels of biological replication, a more thorough analysis of errors and false discovery rates, and an analysis of response patterns using gene network models. Zebrafish embryos were exposed from 1.5 h post-fertilization for 72 h to ecotoxicants representing different classes-2,4-dichlorophenol, 3,4-dichloroaniline, pentachlorophenol, and cadmium chloride-at low concentrations producing a developmental disturbance to 10% of embryos and half of this dose. Extracted whole embryo RNA was then analyzed on microarrays. Analysis revealed responses of 3000-5000 genes, which is 10-1000 times greater than previously reported, with significance at lower levels of fold change. Some gene responses were common to multiple toxicants, and others were restricted to just one or two toxicants. The gene expression profiles for the different toxicants were distinctive, and analysis using network-based models provided a high level of detail of affected processes, some of which were novel. This approach provides a more highly refined view of toxic effects, from which meaningful patterns of response can be discerned and related to functional deficits and from which more reliable indicators of toxicological effect can be predicted.

A protocol has been developed for the separation of brush-border membrane (BBM) and basolateral membrane (BLM) fractions from the kidneys of the roach (Rutilus rutilus) and the Arctic char (Salvelinus alpinus), based on differential precipitation and differential centrifugation. Steady state polarization fluorescence was used to measure membrane fluidity in BBM and BLM from the kidneys of cold- and warm-acclimated fish. The "homeoviscous response" (%HR) in the BLM of cold-acclimated S. alpinus was about four fold higher (78.2%) than in the BLM of cold-acclimated R. rutilus. No %HR was shown by the BBM of R. rutilus, but a fairly strong one (54.3%) by the BBM of S. alpinus. Acclimation temperature had no effect on thermal stabilit, of the (Na⁺ + K⁺)-ATPase from kidney microsomes of S. alpinus, but the preincubation temperature that resulted in 50% inactivation $(LT_{50})$ of the same enzyme was significantly (> 2° C) lower in coldthan in warm-acclimated R. rutilus. No changes or only slight changes of ther...