Seasonal Variations in Clock‐Gene Expression in Atlantic Salmon (Salmo salar)

A circadian clock controls the daily function of the intestine in rainbow trout. Influence of light and food as synchronizers

Environmental factors (daily light/dark cycles, food availability, etc.) entrain endogenous oscillators in living organisms, thereby allowing them to control the rhythms of behavioral and physiological functions, such as energy homeostasis. The gastrointestinal tract (GIT) is the first site of nutrient contact upon food intake. Thus, the GIT is key in energy homeostasis. Circadian oscillators exist within the GIT of mammals, modulating the daily function of the tissue. However, little information in this respect is available for other vertebrates, such as fish. Thus, we aimed to confirm the presence of a circadian oscillator within the GIT of rainbow trout (Oncorhynchus mykiss) and its interaction with locally released hormones that participate in feeding regulation in this species. We subsequently evaluated the role of food and light in synchronizing the rhythmic functioning of the GIT. According to our results, a circadian oscillator exists throughout the GIT of rainbow trout, based on the daily rhythms of clock gene (clock1a, bmal1b, per1, cry2 and reb-ervβ-like) mRNA abundance. Light influences the function of the circadian oscillator within the GIT, but food is a key factor as a synchronizer. The feeding time and the presence and/or absence of food synchronize the rhythmic function of the GIT, as observed for GIT hormones (Ghrelin, Glp1 and Cck). Understanding the functioning of the circadian machinery in peripheral organs such as the GIT will ultimately help to improve different aspects of aquaculture, from farming strategies to welfare, among others.

Seasonal mRNA Expression of Circadian Clock Genes in the Lizard Brain

Seasonally breeding animals undergo physiological and behavioral changes to time reproduction to occur during specific seasons. These changes are regulated by changing environmental conditions, which may be communicated to the brain using the central circadian clock. This clock consists of a daily oscillation in the expression of several core genes, including period (per), cryptochrome (cry), circadian locomotor output cycles kaput (clock), and basic helix-loop-helix ARNT-like protein 1 (bmal1). We began to examine seasonal regulation of four core circadian clock genes in a dissection of the reptile brain containing the hypothalamus-per1, cry1, bmal1 and clock. Our study focused on examining mRNA expression in the morning and compared levels between breeding and nonbreeding animals. We found that per1 and bmal1 mRNA expression was highest in the nonbreeding compared to breeding season in the anole hypothalamus. We also found that cry1 mRNA expression was higher in the female compared to the male anole hypothalamus. We found support for the idea that core circadian genes play a role in regulating changes between the seasons and/or sexes, although more work is needed to elucidate what processes might be differentially regulated. To our knowledge, this is the first examination of the expression of these four genes in the reptilian brain.

Rapid genetic adaptation to a novel ecosystem despite a large founder event

Introduced and invasive species make excellent natural experiments for investigating rapid evolution. Here, we describe the effects of genetic drift and rapid genetic adaptation in pink salmon (Oncorhynchus gorbuscha) that were accidentally introduced to the Great Lakes via a single introduction event 31 generations ago. Using whole-genome resequencing for 134 fish spanning five sample groups across the native and introduced range, we estimate that the source population's effective population size was 146,886 at the time of introduction, whereas the founding population's effective population size was just 72-a 2040-fold decrease. As expected with a severe founder event, we show reductions in genome-wide measures of genetic diversity, specifically a 37.7% reduction in the number of SNPs and an 8.2% reduction in observed heterozygosity. Despite this decline in genetic diversity, we provide evidence for putative selection at 47 loci across multiple chromosomes in the introduced populations, including missense variants in genes associated with circadian rhythm, immunological response and maturation, which match expected or known phenotypic changes in the Great Lakes. For one of these genes, we use a species-specific agent-based model to rule out genetic drift and conclude our results support a strong response to selection occurring in a period gene (per2) that plays a predominant role in determining an organism's daily clock, matching large day length differences experienced by introduced salmon during important phenological periods. Together, these results inform how populations might evolve rapidly to new environments, even with a small pool of standing genetic variation.

Cloning, tissue distribution, and effects of different circadian rhythms on the mRNA expression levels of circadian clock genes Per1a and Per1b in Phoxinus lagowskii

This study describes the cloning and characterization of Period 1a and Period 1b genes and the analysis of their mRNA and protein expression in Amur minnow (Phoxinus lagowskii) after exposure to different light cycles. The full-length P. lagowskii Per1a and Per1b genes encode proteins consisting of 1393 and 1409 amino acids, and share high homology with the per1 genes of other freshwater fish species. The Per1a and Per1b genes were widely expressed within the brain, eye, and peripheral tissues. The acrophase of the Per1a gene in the pituitary gland occurred during the dark phase at ZT15 (zeitgeber time 15, 12 L: 12 D) and ZT18 (8 L, 16 D), whereas the acrophase of the Per1b gene in the pituitary gland was observed during the light phase. Our study suggests that the expression of Per1a and Per1b in P. lagowskii varied depending on differences in circadian rhythm patterns. The results of our dual-luciferase reporter assays demonstrated that the P. lagowskii Per1b gene enhances the activation of NF-κB. This study is the first to examine the circadian clock gene Per1a and Per1b in the high-latitude fish P. lagowskii, offering valuable insights into the effects of different light periods on this fish species.

Adaptive photoperiod interpretation modulates phenological timing in Atlantic salmon

Photoperiod, the portion of 24-h cycle during which an organism is exposed to illumination, is an important phenological cue in many animals. However, despite its influence on critical biological processes, there remain many unknowns regarding how variations in light intensity translate into perceived photoperiod. This experiment examined how light intensity variations affect perceived photoperiod in Atlantic salmon (Salmo salar) to determine whether photoperiod interpretation is, a) fixed such that anything above a minimum detection threshold is regarded as 'illumination', or b) adaptive and varies with recent light exposure. To do this we compared the frequency of smoltification and sexual maturation between groups of male parr which were exposed to one of eight light regimes on a 12:12 cycling regime (12-hour day/12-hour night). The eight regimes were divided into two treatments, four with 'High' daytime light intensity and four with 'Low' daytime light intensity. The 'High' and 'Low' intensity treatments were each sub-divided into four groups for which the subjective 'night' light intensity was 100%, 10%, 1% and 0% of the daytime light intensity, with four replicate tanks of each treatment. The results show that above a minimum detection threshold, Atlantic salmon have adaptive photoperiod interpretation which varies with recent light exposure, and that adaptive photoperiod interpretation modulates the timing of the parr-smolt transformation and sexual maturation. Further, we show that photoperiod interpretation varies between closely related families. Given the influence of phenological timing on species survival, our results reveal a critical role for integration of photoperiod interpretation in attempts to understand how geographically shifting thermal niches due to climate change will affect future populations.

Changes of the clock gene expression in central and peripheral organs of common carp exposed to constant lighting conditions

In both mammals and fish, the circadian system is composed of oscillators that function at the cellular, tissue, and system levels and show the cyclic expression of clock genes. The organization and functioning of the biological clock in fish has not yet been characterized in detail, therefore, in the present study, an extensive analysis of the rhythmic expression of the main components of the biological clock in the central and peripheral organs of common carp was performed. The diurnal changes in clock gene expression were determined with respect to the subjective light cycle in fish exposed to constant light or darkness. It was found that the pattern of expression of clock, bmal, per and cry genes in carp was highest in the brain, pituitary gland, and retina. The peak clock and bmal expression was phase aligned with the lights off, whereas both per genes show similar phasing with acrophase close to light onset. The expression of cry genes varied depending on the type of tissue and the subtype of gene. The diurnal changes in the expression of clock genes demonstrates that, in particular, the expression of the clock in the retina shows endogenous oscillations independent of the influence of light. The data suggest that in carp, the time-varying expression of individual genes allows for a diverse and tissue-specific response to secure oscillations with variable phase and period.

Rhythmic Clock Gene Expression in Atlantic Salmon Parr Brain

To better understand the complexity of clock genes in salmonids, a taxon with an additional whole genome duplication, an analysis was performed to identify and classify gene family members (clock, arntl, period, cryptochrome, nr1d, ror, and csnk1). The majority of clock genes, in zebrafish and Northern pike, appeared to be duplicated. In comparison to the 29 clock genes described in zebrafish, 48 clock genes were discovered in salmonid species. There was also evidence of species-specific reciprocal gene losses conserved to the Oncorhynchus sister clade. From the six period genes identified three were highly significantly rhythmic, and circadian in their expression patterns (per1a.1, per1a.2, per1b) and two was significantly rhythmically expressed (per2a, per2b). The transcriptomic study of juvenile Atlantic salmon (parr) brain tissues confirmed gene identification and revealed that there were 2,864 rhythmically expressed genes (p < 0.001), including 1,215 genes with a circadian expression pattern, of which 11 were clock genes. The majority of circadian expressed genes peaked 2 h before and after daylight. These findings provide a foundation for further research into the function of clock genes circadian rhythmicity and the role of an enriched number of clock genes relating to seasonal driven life history in salmonids.

Diversified regulation of circadian clock gene expression following whole genome duplication

Across taxa, circadian control of physiology and behavior arises from cell-autonomous oscillations in gene expression, governed by a networks of so-called ‘clock genes’, collectively forming transcription-translation feedback loops. In modern vertebrates, these networks contain multiple copies of clock gene family members, which arose through whole genome duplication (WGD) events during evolutionary history. It remains unclear to what extent multiple copies of clock gene family members are functionally redundant or have allowed for functional diversification. We addressed this problem through an analysis of clock gene expression in the Atlantic salmon, a representative of the salmonids, a group which has undergone at least 4 rounds of WGD since the base of the vertebrate lineage, giving an unusually large complement of clock genes. By comparing expression patterns across multiple tissues, and during development, we present evidence for gene- and tissue-specific divergence in expression patterns, consistent with functional diversification of clock gene duplicates. In contrast to mammals, we found no evidence for coupling between cortisol and circadian gene expression, but cortisol mediated non-circadian regulated expression of a subset of clock genes in the salmon gill was evident. This regulation is linked to changes in gill function necessary for the transition from fresh- to sea-water in anadromous fish. Overall, this analysis emphasises the potential for a richly diversified clock gene network to serve a mixture of circadian and non-circadian functions in vertebrate groups with complex genomes.

The generation of daily (circadian) rhythms in behaviour and physiology depends on the activities of networks of so-called clock genes. In vertebrates, these have become highly complex due to a process known as whole genome duplication, which has occurred repeatedly during evolutionary history, giving rise to additional copies of key elements of the clock gene network. It remains unclear whether this results in functional redundancy, or whether it has permitted new roles for clock genes to emerge. Here, based on studies in the Atlantic salmon, a species with an unusually large complement of clock genes, we present evidence in favour of the latter scenario. We observe marked tissue-specific, and developmentally-dependent differences in the expression patterns of duplicated copies of key clock genes, and we identify a subset of clock genes whose expression is associated with the physiological preparation to migrate to sea, but is independent of circadian regulation. Associated with this, cortisol secretion is uncoupled from circadian organisation, contrasting with the situation in mammals. Our results indicate that whole genome duplication has permitted clock genes to diversify into non-circadian functions, and raise interesting questions about the ubiquity of mammal-like coupling between circadian and endocrine function.

Season dependent effects of urban environment on circadian clock of tree sparrow (Passer montanus)

Great efforts have been made recently to understand the effect(s) of urban environments on the circadian and seasonal physiology of wild animals, but the mechanisms involved remain largely unknown.

Discovery of differentially expressed genes in the intestines of Pelteobagrus vachellii within a light/dark cycle

In aquaculture, it is necessary to determine of the diurnal biological variations in the intestines to determine an appropriate feeding schedule. The present study aimed to examine the transcriptomes of the Pelteobagrus vachellii intestines at four time points (0 h, 6 h, 12 h, and 18 h) within a light/dark cycle. In comparison with the zeitgeber time 0 (ZT0) transcriptomes, we identified 37,842 unigenes with significant differential expression, including 6,638; 9,626; and 7,938 that genes upregulated, and 3,507; 4,703; and 5,412 genes that were down regulated at 4, 12, and 24 h respectively. The differentially expressed unigenes were subjected to enrichment analysis, which indicated the involvement of the major digestive pathways, including digestion of protein, lipid and carbohydrate, catabolic process (protein, carbohydrate and lipid), and circadian rhythm. We selected 73 key differentially expressed genes (DEGs) from among these pathways and identified DEGs that showed increased expression at night, including those encoding trypsin-3, chymotrypsinogen 2, amino acid transporter, maltase-glucoamylase, facilitated glucose transporter, lipase, phospholipase, fatty acid-binding protein, fatty acid synthase, long-chain fatty acid transport protein, and apolipoprotein. Moreover, DEGs involved of circadian rhythm were identified, including brain-muscle-Arnt-like 1 (BMAL1), cryptochrome-1, circadian locomoter output cycles protein kaput (CLOCK) and period circadian protein homolog 1-3. Finally, the expression levels of 12 unigenes were analyzed using quantitative real-time PCR, which were in accordance with RNA-sequencing analysis. In general, the expression of genes related to the digestion of proteins, lipids, and carbohydrates showed upregulated expression at night; however, the peak time of expression of transporters for different nutrition molecules showed more diversification within the light/dark cycle.

Daily expression of a clock gene in the brain and pituitary of the Malabar grouper (Epinephelus malabaricus)

Recent studies have revealed that, in addition to regulating the circadian system, clock genes such as cryptochrome (Cry) genes are involved in seasonal and lunar rhythmicity in fish. This study clarified the transcriptional characteristics of a Cry subtype (mgCry2) in the brain of the Malabar grouper, Epinephelus malabaricus, which is an important aquaculture species that spawns around the new moon. The cDNA sequence of mgCry2 showed high identity (97-99%) with fish Cry2 and had an open reading frame encoding a protein with 170 amino acids. Phylogenetic analyses revealed that mgCRY2 had high identity with CRY in other fish species. Real-time quantitative polymerase chain reaction (qPCR) showed the widespread distribution of mgCry2 in neural (brain, pituitary, and retina) and peripheral (heart, liver, kidney, spleen, gill, intestine, and ovary) tissues. When immature Malabar groupers were reared under a light-dark cycle (LD = 12:12) and the amounts of mgCry2 mRNA in the telencephalon and diencephalon were measured at 4-h intervals, the levels increased during photophase and decreased during scotophase. Day-night variation in mgCry2 mRNA abundance was also observed in the pituitary. These daily profiles suggest that mgCry2 is a light-responsive gene in neural tissues. In situ hybridization analyses showed that mgCry2 was strongly transcribed in the nucleus lateralis tuberis of the ventral hypothalamus, peripheral area of the proximal pars distalis, and the pars intermedia of the pituitary. We conclude that clock genes expressed in the pituitary and diencephalon play a role in entraining the endocrine network of the Malabar grouper to periodic changes in external cues.

SIRT1 mediates the effect of stress on hypothalamic clock genes and food intake regulators in rainbow trout, Oncorhynchus mykiss

Stress negatively affects a wide range of physiological and behavioural functions (circadian physiology and food intake, among others), thus compromising animal welfare. Cortisol mediates the effect of stress on food intake, but other mediators (such as sirtuins) may participate in that related to circadian physiology. We evaluated 1) the effect of stress on the day-night variation of hypothalamic clock genes and food intake regulators, 2) changes of mRNA abundance in cortisol biosynthesis at the head kidney, and 3) changes of glucocorticoid receptors in both tissues of rainbow trout, together with the involvement of SIRT1 in such effect. Trout receiving or not SIRT1 inhibitor (EX527) and subjected or not to stress by high stocking density (72 h), were sampled at day- (ZT10) and night-time (ZT18). Our results indicate that SIRT1 mediates the effect of stress on mRNA abundance of clock genes in trout hypothalamus, but it also influences those changes occurring on food intake-related peptides. High stocking density inhibits clock genes expression, but enhances that of food intake-related peptides. EX527 treatment prevents stress-related changes observed in clock genes, thus evidencing a key role played by SIRT1 in mediating this effect on trout circadian oscillators. On the other hand, EX527 treatment partially prevents changes of food intake-related peptides, indicating that an interaction between SIRT1 and other mediators (such as cortisol) exists during response to stress. In support of that, our results reveal that SIRT1 influences cortisol biosynthesis during stress. Whatever the case is, further research will help understanding the underlying mechanisms involved.

Testing the expression of circadian clock genes in the tissues of Chinook salmon, Oncorhynchus tshawytscha

Animals have an endogenous circadian clock that temporally regulates 24 hour (h) oscillations in behavior and physiology. This highly conserved mechanism consists of two positive regulators, Bmal and Clock, and two negative regulators, Cry and Per, that run with a 24-h cycle that synchronizes itself with environmental changes in light, food, and temperature. We examined the circadian clock in Chinook salmon (Oncorhynchus tshawytscha), a non-model organism in which the function of the clock has not been studied. Recent studies indicate that clock genes in Chinook salmon play a role in its evolution of local adaptation, possibly by influencing migration timing. We designed real-time quantitative PCR (RT-qPCR) assays to quantify the transcription of components of the clock system, and validated these for PCR efficiency and specificity in detecting Chinook target genes. Chinook salmon tissue samples were collected in 3-h intervals, over the course of 24 h, from five different organs. Our data indicate that the circadian clock functions differently in each of these tissues. In the liver, positive and negative regulators exhibit anti-phasic peaking in the evening and morning, respectively. However, in the heart, these same regulators peak and trough with a different timing, indicating that the liver and heart are not synchronous. The digestive tract displays yet another difference: simultaneous phases in the expression of positive and negative clock regulators, and we do not observe significant rhythms in clock gene expression in the retina. Our data show that there is a functional clock in Chinook salmon tissues, but that this clock behaves in a tissue-specific manner, regardless of the whole animal being exposed to the same environmental cues. These results highlight the adaptive role of the clock in Chinook salmon and that it may have different positive and negative effects depending on tissue function.

Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments

There is a paucity of information on the physiological changes that occur over the course of salmon early marine migration. Here we aim to provide insight on juvenile Coho salmon (Oncorhynchus kisutch) physiology using the changes in gene expression (cGRASP 44K microarray) of four tissues (brain, gill, muscle, and liver) across the parr to smolt transition in freshwater and through the first eight months of ocean residence. We also examined transcriptome changes with body size as a covariate. The strongest shift in the transcriptome for brain, gill, and muscle occurred between summer and fall in the ocean, representing physiological changes that we speculate may be associated with migration preparation to feeding areas. Metabolic processes in the liver were positively associated with body length, generally consistent with enhanced feeding opportunities. However, a notable exception to this metabolic pattern was for spring post-smolts sampled soon after entry into the ocean, which showed a pattern of gene expression more likely associated with depressed feeding or recent fasting. Overall, this study has revealed life stages that may be the most critical developmentally (fall post-smolt) and for survival (spring post-smolt) in the early marine environment. These life stages may warrant further investigation.

Involvement of cortisol and sirtuin1 during the response to stress of hypothalamic circadian system and food intake-related peptides in rainbow trout, Oncorhynchus mykiss

Stress is conditioning animal welfare by negatively affecting a wide range of physiological and behavioral functions. This may be applied to circadian physiology and food intake. Cortisol, the stress-related hormone, may mediate such effect of stress, but other indirect mediators might be considered, such as sirtuin1. Then, either the independent modulatory effect or the existence of any interaction between mediators may be responsible. The circadian system is the main modulator of several integrative mechanisms at both central and peripheral levels that are rhythmically presented, thus influencing different processes such as food intake. In this way, food intake is controlled by the circadian system, as demonstrated by the persistence of such rhythms of food intake in the absence of environmental external cues. Our study aimed to evaluate the daily profile of hypothalamic mRNA abundance of circadian clock genes (clock1a, bmal1, per1 and rev-erbβ-like), and food intake regulators (crf, pomc-a1, cart, and npy) in rainbow trout (Oncorhynchus mykiss), the impact of stress on such rhythms, and the involvement of cortisol and sirtuin1 as mediators. Four cohorts of trout were subjected to 1) normal stocking density (control group), 2) high stocking density for 72 hours (stress group), 3) normal stocking density and implanted with mifepristone, a glucocorticoid receptors antagonist, and 4) mifepristone administered and stressed for 72 hours. Fish from each group were sampled every 4-h along the 24-h LD cycle, and cortisol, glucose and lactate plasma levels were evaluated. Hypothalamic mRNA abundance of clock genes, food intake regulators, glucocorticoid receptors and sirtuin1 were qPCR assayed. Our results reveal the impact of stress on most of the genes assayed, but different mechanisms appear to be involved. The rhythm of clock genes displayed decreased amplitude and averaged levels in stressed trout, with no changes of the acrophase being observed. This effect was not prevented by mifepristone. On the contrary, the effect of stress on the daily profile of crf, pomc-a1, and npy was totally prevented by mifepristone administration. Accordingly, cortisol appears to mainly mediate the effect of stress on food intake regulators through binding to specific glucocorticoid receptors within trout hypothalamus, whereas sirtuin1 is apparently mediating such effects on the circadian system in the same brain region. Further research must be performed to clarify those mechanisms through which stress influences food intake and the circadian oscillator within the same brain region, hypothalamus, in rainbow trout, and the interaction among them all.

Interplay between the endocrine and circadian systems in fishes

The circadian system is responsible for the temporal organisation of physiological functions which, in part, involves daily cycles of hormonal activity. In this review, we analyse the interplay between the circadian and endocrine systems in fishes. We first describe the current model of fish circadian system organisation and the basis of the molecular clockwork that enables different tissues to act as internal pacemakers. This system consists of a net of central and peripherally located oscillators and can be synchronised by the light-darkness and feeding-fasting cycles. We then focus on two central neuroendocrine transducers (melatonin and orexin) and three peripheral hormones (leptin, ghrelin and cortisol), which are involved in the synchronisation of the circadian system in mammals and/or energy status signalling. We review the role of each of these as overt rhythms (i.e. outputs of the circadian system) and, for the first time, as key internal temporal messengers that act as inputs for other endogenous oscillators. Based on acute changes in clock gene expression, we describe the currently accepted model of endogenous oscillator entrainment by the light-darkness cycle and propose a new model for non-photic (endocrine) entrainment, highlighting the importance of the bidirectional cross-talking between the endocrine and circadian systems in fishes. The flexibility of the fish circadian system combined with the absence of a master clock makes these vertebrates a very attractive model for studying communication among oscillators to drive functionally coordinated outputs.

Daily feeding and protein metabolism rhythms in Senegalese sole post-larvae

Fish hatcheries must adapt larval feeding protocols to feeding behavior and metabolism patterns to obtain more efficient feed utilization. Fish larvae exhibit daily ingesting rhythms rather than ingesting food continuously throughout the day. The aim of this study was to determine the daily patterns of feed intake, protein digestibility, protein retention and catabolism in Senegalese sole post-larvae (Solea senegalensis; 33 days post-hatching) using 14C-labeled Artemia protein and incubation in metabolic chambers. Sole post-larvae were fed at 09:00, 15:00, 21:00, 03:00 and 09:00+1 day; and those fed at 09:00, 21:00, 03:00 and 09:00+1 day showed significantly higher feed intake than post-larvae fed at 15:00 h (P=0.000). Digestibility and evacuation rate of ingested protein did not change during the whole cycle (P=0.114); however, post-larvae fed at 21:00 and 03:00 h showed the significantly highest protein retention efficiency and lowest catabolism (P=0.002). Therefore, results confirm the existence of daily rhythmicity in feeding activity and in the utilization of the ingested nutrients in Senegalese sole post-larvae.

Sequencing and characterization of a multi-organ Arctic charr transcriptome: A toolbox for investigating polymorphism and seasonal life in a high Arctic fish

The Arctic charr (Salvelinus alpinus L.) inhabits fresh water ecosystems of the high North. The species has developed a strong phenotypic plasticity and variability in life history characteristics which has made this species an attractive model for investigations on phenotype plasticity, morph formation and ecological speciation. Further, the extreme seasonal variations in environmental conditions (e.g. food availability) in the high North induce seasonal changes in phenotype, which require precise timing mechanisms and physiological preparations. Individual gating of life-history strategies (e.g. formation of resident and sea-migrating morphs) and transitions (e.g. maturation) depends on conditional traits (size/energy status) at specific assessment time windows, and complex neuroendocrine regulation, which so far is poorly understood. In the absence of a reference genome, and in order to facilitate the investigation of the complex biological mechanisms of this unique fish model, the present study reveals a reference transcriptome for the Arctic charr. Using Roche 454 GS FLX+, we targeted various organs being either at the crossroads of many key pathways (neuroendocrine, metabolic, behavioral), of different ontological origins or displaying complementary physiological functions. The assemblage yielded 34,690 contigs greater than 1000bp with an average length (1690bp) and annotation rate (52%) within the range, or even higher, than what has been previously obtained with other teleost de novo transcriptomes. We dramatically improve the publically available transcript data on this species that may indeed be useful for various disciplines, from basic research to applied aspects related to conservation issues and aquaculture.

Circadian rhythms of clock gene expression in Nile tilapia (Oreochromis niloticus) central and peripheral tissues: influence of different lighting and feeding conditions

The present research aimed to investigate the existence of clock gene expression rhythms in tilapia, their endogenous origin, and how light and feeding cycles synchronize these rhythms. In the first experiment, two groups of fish were kept under an LD cycle and fed at two different time points: in the middle of the light (ML) or in the middle of the dark (MD) phase. In the second experiment, fish fed at ML was fasted and kept under constant lighting (LL) conditions for 1 day. In both experiments, the samples from central (optic tectum and hypothalamus) and peripheral (liver) tissues were collected every 3 h throughout a 24 h cycle. The expression levels of clock genes bmal1a, clock1, per1b, cry2a, and cry5 were analyzed by quantitative PCR. All the clock genes analyzed in brain regions showed daily rhythms: clock1, bmal1a, and cry2a showed the acrophase approximately at the end of the light phase (ZT 8:43-11:22 h), whereas per1b and cry5 did so between the end of the dark phase and the beginning of the light phase, respectively (ZT 21:16-4:00 h). These rhythms persisted under constant conditions. No effect of the feeding time was observed in the brain. In the liver, however, the rhythms of clock1 and cry5 were influenced by feeding, and a shift was observed in the MD fish group (ZT 3:58 h for clock1 and 11:20 h for cry5). This study provides the first insights into the molecular clock of tilapia, a very important fish species for aquaculture. It also reveals the endogenous origin of clock gene rhythms and the ability of feeding time to shift the phase in some clock genes in the peripheral, but not the central, oscillator.

The liver of goldfish as a component of the circadian system: Integrating a network of signals

The circadian system drives daily physiological and behavioral rhythms that allow animals to anticipate cyclic environmental changes. The discovery of the known as "clock genes", which are very well conserved through vertebrate phylogeny, highlighted the molecular mechanism of circadian oscillators functioning, based on transcription and translation cycles (∼ 24 h) of such clock genes. Studies in goldfish have shown that the circadian system in this species is formed by a net of oscillators distributed at central and peripheral locations, as the retina, brain, gut and liver, among others. In this work we review the existing information about the hepatic oscillator in goldfish due to its relevance in metabolism, and its key role as target of a variety of humoral signals. Different input signals modify the molecular clockwork in the liver of goldfish. Among them, there are environmental cues (photocycle and feeding regime) and different encephalic and peripheral endogenous signals (orexin, ghrelin and glucocorticoids). Per clock genes seem to be a common target for different signals. Thus, this genes family might be important for shifting the hepatic oscillator. The physiological relevance of the crosstalking between metabolic and feeding-related hormones and the hepatic clock sets the stage for the hypothesis that these hormones could act as "internal zeitgebers" communicating oscillators in the goldfish circadian system.

Seasonal effects on gene expression

Many health conditions, ranging from psychiatric disorders to cardiovascular disease, display notable seasonal variation in severity and onset. In order to understand the molecular processes underlying this phenomenon, we have examined seasonal variation in the transcriptome of 606 healthy individuals. We show that 74 transcripts associated with a 12-month seasonal cycle were enriched for processes involved in DNA repair and binding. An additional 94 transcripts demonstrated significant seasonal variability that was largely influenced by blood cell count levels. These transcripts were enriched for immune function, protein production, and specific cellular markers for lymphocytes. Accordingly, cell counts for erythrocytes, platelets, neutrophils, monocytes, and CD19 cells demonstrated significant association with a 12-month seasonal cycle. These results demonstrate that seasonal variation is an important environmental regulator of gene expression and blood cell composition. Notable changes in leukocyte counts and genes involved in immune function indicate that immune cell physiology varies throughout the year in healthy individuals.

Daily and seasonal expression of clock genes in the pituitary of the European sea bass (Dicentrarchus labrax)

The expression of select clock genes (clock, bmal, per1, per2, cry1, cry2) was investigated throughout the day and across the four seasons for two consecutive years in the pituitary of adult sea bass (Dicentrarchus labrax). A rhythmic pattern of daily expression was consistently observed in summer and autumn, while arrhythmicity was observed for some clock genes during spring and winter, concomitant with low water temperatures. The expression of clock and bmal showed highest values at the end of the day and during the night, while that of per and cry was mostly antiphasic, with high values during the day. Melatonin affects clock-gene expression in the pituitary of mammals. We therefore sought to test the effect of melatonin on clock-gene expression in the pituitary of sea bass both in vivo and in vitro. Melatonin modestly affected the expression of some clock genes (in particular cry genes) when added to the fish diet or the culture medium of pituitary glands. Our data show that clock genes display rhythmic daily expression in the pituitary of adult sea bass, which are profoundly modified according to the season. We suggest that the effect of photoperiod on clock gene expression may be mediated, at least in part, by melatonin, and that temperature may have a key role adjusting seasonal variations.

Daily rhythms in expression of genes of hepatic lipid metabolism in Atlantic salmon (Salmo salar L.)

In mammals, several genes involved in liver lipid and cholesterol homeostasis are rhythmically expressed with expression shown to be regulated by clock genes via Rev-erb 1α. In order to elucidate clock gene regulation of genes involved in lipid metabolism in Atlantic salmon (Salmo salar L.), the orphan nuclear receptor Rev-erb 1α was cloned and 24 h expression of clock genes, transcription factors and genes involved in cholesterol and lipid metabolism determined in liver of parr acclimated to a long-day photoperiod, which was previously shown to elicit rhythmic clock gene expression in the brain. Of the 31 genes analysed, significant daily expression was demonstrated in the clock gene Bmal1, transcription factor genes Srebp1, Lxr, Pparα and Pparγ, and several lipid metabolism genes Hmgcr, Ipi, ApoCII and El. The possible regulatory mechanisms and pathways, and the functional significance of these patterns of expression were discussed. Importantly and in contrast to mammals, Per1, Per2, Fas, Srebp2, Cyp71α and Rev-erb 1α did not display significant daily rhythmicity in salmon. The present study is the first report characterising 24 h profiles of gene expression in liver of Atlantic salmon. However, more importantly, the predominant role of lipids in the nutrition and metabolism of fish, and of feed efficiency in determining farming economics, means that daily rhythmicity in the regulation of lipid metabolism will be an area of considerable interest for future research in commercially important species.

Comparative study of pineal clock gene and AANAT2 expression in relation to melatonin synthesis in Atlantic salmon (Salmo salar) and European seabass (Dicentrarchus labrax)

The photoreceptive teleost pineal is considered to be essential to the generation, synchronisation and maintenance of biological rhythms, primarily via melatonin release. The role of internal (circadian clock) and external (light) signals controlling melatonin production in the fish pineal differs between species, yet the reasons underpinning this remain largely unknown. Whilst in salmonids, pineal melatonin is apparently regulated directly by light, in all other studied teleosts, rhythmic melatonin production persists endogenously under the regulation of clock gene expression. To better understand the role of clocks in teleost pineals, this study aimed to characterise the expression of selected clock genes in vitro under different photoperiodic conditions in comparison to in vivo in both Atlantic salmon (Salmo salar) and in European seabass (Dicentrarchus labrax) (in vitro 12L:12D), a species known to display endogenous rhythmic melatonin synthesis. Results revealed no rhythmic clock gene (Clock, Period 1 &2) expression in Atlantic salmon or European seabass (Clock and Period 1) pineal in vitro. However rhythmic expression of Cryptochrome 2 and Period 1 in the Atlantic salmon pineal was observed in vivo, which infers extra-pineal regulation of clocks in this species. No rhythmic arylalkylamine N-acetyltransferase 2 (Aanat2) expression was observed in the Atlantic salmon yet in the European seabass, circadian Aanat2 expression was observed. Subsequent in silico analysis of available Aanat2 genomic sequences reveals that Atlantic salmon Aanat2 promoter sequences do not contain similar regulatory architecture as present in European seabass, and previously described in other teleosts which alludes to a loss in functional connection in the pathway.

Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

Neutral genetic markers are routinely used to define distinct units within species that warrant discrete management. Human-induced changes to gene flow however may reduce the power of such an approach. We tested the efficiency of adaptive versus neutral genetic markers in differentiating temporally divergent migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid high gene flow owing to artificial propagation and habitat alteration. We compared seven putative migration timing genes to ten microsatellite loci in delineating three migratory groups of Chinook in the Feather River, CA: offspring of fall-run hatchery broodstock that returned as adults to freshwater in fall (fall run), spring-run offspring that returned in spring (spring run), and fall-run offspring that returned in spring (FRS). We found evidence for significant differentiation between the fall and federally listed threatened spring groups based on divergence at three circadian clock genes (OtsClock1b, OmyFbxw11, and Omy1009UW), but not neutral markers. We thus demonstrate the importance of genetic marker choice in resolving complex life history types. These findings directly impact conservation management strategies and add to previous evidence from Pacific and Atlantic salmon indicating that circadian clock genes influence migration timing.

Fish sleeping under sandy bottom: interplay of melatonin and clock genes

Wrasse species exhibit a definite daily rhythm in locomotor activity and bury themselves in the sand at the bottom of the ocean at night. It remains unclear how their behavior in locomotor activity is endogenously regulated. The aim of the present study was to clarify the involvement of melatonin and clock genes (Per1, Per2, Bmal1, and Cry1) in daily and circadian rhythms of the threespot wrasse, Halichoeres trimaculatus, which is a common species in coral reefs. Daily and circadian rhythms in locomotor activity were monitored under conditions of light-dark cycle (LD=12:12), constant light (LL), and darkness (DD). Daily rhythms in locomotor activity were observed under LD and persisted under LL and DD. Melatonin from a cultured pineal gland showed daily variations with an increase during the nighttime and a decrease during daytime, which persisted under DD. Melatonin treatment induced decreases in locomotor activity and respiratory rate, suggesting that melatonin has a sleep-inducing effect. Per1 and Per2 mRNA abundance in the brain under LD showed daily rhythms with an increase around lights on. Robust oscillation of Per1 and Per2 mRNA expression persisted under DD and LL, respectively. Expression of Bmal1 and Cry1 mRNA also showed daily and circadian patterns. These results suggest that clock genes are related to circadian rhythms in locomotor activity and that melatonin plays a role in inducing a sleep-like state after fish bury themselves in the sand. We conclude that the sleep-wake rhythm of the wrasse is regulated by a coordination of melatonin and clock genes.

Daily rhythmic expression patterns of clock1a, bmal1, and per1 genes in retina and hypothalamus of the rainbow trout, Oncorhynchus mykiss

Living organisms show daily rhythms in physiology, behavior, and gene expression, which are due to the presence of endogenous clocks that synchronize biological processes to the 24-h light/dark cycle. In metazoans, generation of circadian rhythmicity is a consequence of specialized tissues known as "master clocks," having different locations among species. A few studies have described clock-gene expression in fish neural tissues, but none of them assessed clock-gene expression in different discrete regions. The present study was designed to explore the presence/absence of circadian clock-gene expression in the rainbow trout (Oncorhynchus mykiss) retina and hypothalamus. Juvenile fish were acclimated to a 12:12 light (L)-dark (D) cycle. Then, retina and hypothalamus were collected from animals kept under LD conditions or constant darkness (DD) for 24 h. Real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) assays were performed to quantify expression of the core circadian genes Clock1a, Bmal1, and Per1 as representative members of the circadian oscillator. All clock genes analyzed in the retina and hypothalamus showed circadian fluctuations. However, gene expression peaked in the rainbow trout hypothalamus with a 3-h (Clock1a and Bmal1) or 6-h (Per1) delay relative to that observed in the retina, the latter showing highest expression levels at zeitgeber times 9 (ZT9) for Clock1a and Bmal1, and at ZT21 for Per1. When exposed to DD, the rhythmic gene expression pattern was maintained for all genes in the rainbow trout retina, but only for Clock1a and Per1 in the hypothalamus. Bmal1 failed to cycle under DD, suggesting that hypothalamic clock function might depend on either several clock-gene isoforms or regulation from external inputs. Overall, these data indicate that representative molecular members of the core circadian clock are present in both the retina and hypothalamus of rainbow trout.

Insulin-like growth factor (IGF) signalling and genome-wide transcriptional regulation in fast muscle of zebrafish following a single-satiating meal

Male zebrafish (Danio rerio) were fasted for 7 days and fed to satiation over 3 h to investigate the transcriptional responses to a single meal. The intestinal content at satiety (6.3% body mass) decreased by 50% at 3 h and 95% at 9 h following food withdrawal. Phosphorylation of the insulin-like growth factor (IGF) signalling protein Akt peaked within 3 h of feeding and was highly correlated with gut fullness. Retained paralogues of IGF hormones genes were regulated with feeding, with igf1a showing a pronounced peak in expression after 3 h and igf2b after 6 h. Igf-I receptor transcripts were markedly elevated with fasting, and decreased to their lowest levels 45 min after feeding. igf1rb transcripts increased more quickly than igf1ra transcripts as the gut emptied. Paralogues of the insulin-like growth factor binding proteins (IGFBPs) were constitutively expressed, except for igfbp1a and igfbp1b transcripts, which were significantly elevated with fasting. Genome-wide transcriptional responses were analysed using the Agilent 44K oligonucleotide microarray and selected genes validated by qPCR. Fasting was associated with the upregulation of genes for the ubiquitin-proteasome degradation pathway, anti-proliferative and pro-apoptotic genes. Protein chaperones (unc45b, hspd1, hspa5, hsp90a.1, hsp90a.2) and chaperone interacting proteins (ahsa1 and stip1) were upregulated 3 h after feeding along with genes for the initiation of protein synthesis and mRNA processing. Transcripts for the enzyme ornithine decarboxylase 1 showed the largest increase with feeding (11.5-fold) and were positively correlated with gut fullness. This study demonstrates the fast nature of the transcriptional responses to a meal and provides evidence for differential regulation of retained paralogues of IGF signalling pathway genes.

Growth and the regulation of myotomal muscle mass in teleost fish

Teleost muscle first arises in early embryonic life and its development is driven by molecules present in the egg yolk and modulated by environmental stimuli including temperature and oxygen. Several populations of myogenic precursor cells reside in the embryonic somite and external cell layer and contribute to muscle fibres in embryo, larval, juvenile and adult stages. Many signalling proteins and transcription factors essential for these events are known. In all cases, myogenesis involves myoblast proliferation, migration, fusion and terminal differentiation. Maturation of the embryonic muscle is associated with motor innervation and the development of a scaffold of connective tissue and complex myotomal architecture needed to generate swimming behaviour. Adult muscle is a heterogeneous tissue composed of several cell types that interact to affect growth patterns. The development of capillary and lymphatic circulations and extramuscular organs--notably the gastrointestinal, endocrine, neuroendocrine and immune systems--serves to increase information exchange between tissues and with the external environment, adding to the complexity of growth regulation. Teleosts often exhibit an indeterminate growth pattern, with body size and muscle mass increasing until mortality or senescence occurs. The dramatic increase in myotomal muscle mass between embryo and adult requires the continuous production of muscle fibres until 40-50% of the maximum body length is reached. Sarcomeric proteins can be mobilised as a source of amino acids for energy metabolism by other tissues and for gonad generation, requiring the dynamic regulation of muscle mass throughout the life cycle. The metabolic and contractile phenotypes of muscle fibres also show significant plasticity with respect to environmental conditions, migration and spawning. Many genes regulating muscle growth are found as multiple copies as a result of paralogue retention following whole-genome duplication events in teleost lineages. The extent to which indeterminate growth, ectothermy and paralogue preservation have resulted in modifications of the genetic pathways regulating muscle growth in teleosts compared to mammals largely remains unknown. This review describes the use of compensatory growth models, transgenesis and tissue culture to explore the mechanisms of muscle growth in teleosts and provides some perspectives on future research directions.

Feeding time synchronizes clock gene rhythmic expression in brain and liver of goldfish (Carassius auratus)

Little is known about the feeding time dependence of clock gene expression in fish. The aim of the present study was to investigate whether a scheduled feeding time can entrain the rhythmic expression of several clock genes (period and cryptocrome) in the brain and liver of a teleost, the goldfish. Fish maintained under continuous light (LL) conditions were divided into 3 groups. Two groups were fed daily at 1000 h and 2200 h, respectively, and the third group was subjected to a random schedule regime. After 30 days, the fishes under 24-h food deprivation were sacrificed through a 24-h cycle, and clock gene expression in the optic tectum, hypothalamus, and liver was quantified by real-time PCR. The findings pointed to differences between the central and peripheral tissues studied. In the absence of a light-dark cycle (constant light), a scheduled feeding regime was necessary and sufficient to maintain both the rhythmic expression of several clock genes in the optic tectum and hypothalamus, as well as daily rhythms in locomotor activity. In contrast, neither locomotor activity nor clock gene expression in brain tissues was synchronized in randomly fed fish. However, in the liver, most of the clock genes studied presented significant daily rhythms in phase (related to the time of the last meal) in all 3 experimental groups, suggesting that the daily rhythm of clock genes in this organ only depends on the last meal time. The data suggest that, as in mammals, the smooth running of the food entrainable oscillator (FEO) in fish involves the rhythmic expression of several clock genes (Per1 and Cry3) in the central and peripheral structures. The results also indicate that the food anticipatory activity (FAA) in goldfish is not only the result of rhythmic clock gene expression in the liver because rhythmic clock gene expression was observed in randomly fed fishes, while FAA was not observed.

Diurnal expression of clock genes in pineal gland and brain and plasma levels of melatonin and cortisol in Atlantic salmon parr and smolts

In Atlantic salmon, the preadaptation to a marine life, i.e., parr-smolt transformation, and melatonin production in the pineal gland are regulated by the photoperiod. However, the clock genes have never been studied in the pineal gland of this species. The aim of the present study was to describe the diurnal expression of clock genes (Per1-like, Cry2, and Clock) in the pineal gland and brain of Atlantic salmon parr and smolts in freshwater, as well as plasma levels of melatonin and cortisol. By employing an out-of-season smolt production model, the parr-smolt transformation was induced by subjecting triplicate groups of parr to 6 wks (wks 0 to 6) under a 12 h:12 h light-dark (LD) regime followed by 6 wks (wks 6 to 12) of continuous light (LL). The measured clock genes in both pineal gland and brain and the plasma levels of melatonin and cortisol showed significant daily variations in parr under LD in wk 6, whereas these rhythms were abolished in smolts under LL in wk 12. In parr, the pineal Per1-like and Cry2 expression peaked in the dark phase, whereas the pineal Clock expression was elevated during the light phase. Although this study presents novel findings on the clock gene system in the teleost pineal gland, the role of this system in the regulation of smoltification needs to be studied in more detail.

Effect of continuous light on daily levels of plasma melatonin and cortisol and expression of clock genes in pineal gland, brain, and liver in atlantic salmon postsmolts

Continuous light is a common practice in salmon farming, where it is used to enhance growth, induce smoltification, and regulate puberty. However, knowledge about how different tissues receive information about daylength is limited. The aim of the present study was to evaluate the daily expression of clock (Per1-like, Cry2, and Clock), the nuclear transcription factor (peroxisome proliferator-activated receptor, PPAR; CCAAT/enhancer binding protein, C/EBP), and the endoplasmic reticulum (ER) stress (protein disulfide isomerase associated 3, PDIA3) genes in the pineal gland, brain, and liver of Atlantic salmon postsmolts reared under 12-h light:12-h dark (LD) regimes or under continuous light (LL) for 6 wks following transfer to seawater. All measured clock mRNAs displayed daily variations in one or more organs under LD, as well as plasma levels of melatonin. Similar variations were noted in the liver c/ebpα, pineal c/ebpδ, and pdia3 mRNAs. Under LL, the clock and nuclear transcription factor mRNAs did not show any daily variation in the studied organs, with the exception of pineal pdia3. Furthermore, LL had the opposite effect on the levels of melatonin and cortisol, as observed by the increase in pineal Clock, Per2, pparα, and c/ebpα and c/ebpδ mRNAs and decrease in liver Clock, Per2, and pparα mRNAs compared to those under LD. The present findings show that the expression of clock genes is affected by the light across organs and that there is a relation between PPAR, C/EBP, and clock mRNAs; however, the functional role of the individual nuclear transcription factors related to this observation remains to be established in the pineal gland and liver. (Author correspondence: Tihu@nifes.no ).