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The study examined the impact of a diet enriched with nanosilver (AgNPs) on the specific immunity, tissue biopsy, and growth effectiveness of Labeo rohita infected with A. carviae. The fish were divided into four groups with replications, and three diets were prepared with AgNPs (0, 10, 15, and 20 µg AgNPs kg-1 diet) added. The fish in the 15µg kg-1 group showed improved growth rates and a 70% survival rate after being challenged with A. carviae. Antioxidant indices, as well as the non-specific immune response, provided notable variations in the inclusion values of AgNPs in the liver and gill. The supplementation of 15µgkg-1 AgNPs most effectively improved tissue damage caused by A. caviae exposure in immunoprotective organs. T3 had higher liver TNF-α transcription than other treatments, while T4 had the highest values for IL-10. The amount of IL-10 in kidneys, gills, and muscles was also higher in T3, T2 and T3 respectively. The research suggests that AgNPs can positively influence fish growth and manage A. caviae infections by boosting antioxidant status and immunity while causing minimal harm to the immunoprotective organs. [ABSTRACT FROM AUTHOR]

Sepiella japonica is a worldwide marine cuttlefish species of high economic value. S. japonica routinely modifying behaviors in reproductive life, such as rapid aging until death after spawning, has been recognized in artificial breeding. However, reproductive behavior at the level of genes is rarely reported, thus, the research on the genetic basis of behavior, reproduction, and artificial breeding was limited. We applied RNA-seq in different stages of reproduction to investigate the reason of rapid aging after spawning, pre-maturity, pre-spawning after maturity, and post-spawning. The retinoid X receptor (RXR) gene family in S. japonica was identified, and 1 343–1 452 differentially expressed genes (DEGs) in all 3 stages of reproductive life were identified from pairwise mRNA comparisons. Furthermore, through the GO term and KEGG analysis, S. japonica could handle neuronal development and network formation before maturity and have a functional degradation of neural communication, signal transduction, vision, and gene expression after spawning. Eight SjRXRαs have been identified and they played different roles in growth development or reproduction. Therefore, the regulation of several channels and receptors is the intrinsic molecular mechanism of rapid aging after spawning in S. japonica. This study revealed the survival strategy and provided fundamental data on the level of genes for understanding the reproductive behavior and the reproduction of S. japonica. [ABSTRACT FROM AUTHOR]

Dayak onion (Eleutherine bulbosa (Mill.) Urb.) has the potential to be an immunostimulant to benefit fish health. This study aimed to evaluate the effectiveness of dietary supplementation with the powder and crude ethanol extracts of Dayak onion on the hematology and immune response parameters of Nile tilapia challenged with Aeromonas hydrophila. The research used a completely randomized design with six treatments and three replications. Nile tilapias were fed with Dayak onion (w/v) consisting of powders of 5% (P5), 10% (P10), and 15% (P15), while crude extract was 0.5% (E05) and given during rearing for 30 days. Positive control (C+) and negative control (C-) were used without Dayak onion. Nile tilapia in treatment C+, P5, P10, and P15 were injected with A. hydrophila 106 CFU mL-1, while that in treatment C- was injected with phosphate buffered saline (PBS) intramuscularly. The results showed that the dietary with 15% powder and 0.5% crude extract significantly improved the hematology and immune response parameters compared to the control after the challenge against A. hydrophila (P<0.05). Dayak onion supplementation effectively increased the health status based on hematology and immune response parameters of Nile tilapia against A. hydrophila infection. [ABSTRACT FROM AUTHOR]

Antigen-presentation via major histocompatibility complex (MHC) to T cells is the key event to initiate adaptive immune responses. In teleosts, as in mammals, the main types of professional antigen-presenting cells (APCs) are dendritic cells (DCs), monocytes/macrophages, and B cells. In the current study, flow cytometry, immunostaining and qPCR have been used to show that neutrophils in the teleost fish Atlantic salmon (Salmo salar L.) have antigen-presenting properties. The neutrophils were positive for MHC class II, CD83 and CD80/86, and upon in vitro bacterial exposure, gene expression analysis of purified neutrophils showed that IL-12p40, which is essential for proliferation of naïve T cells, was highly upregulated at both 6 and 24 h post bacterial exposure. Based on presence of MHC class II and upregulation of molecules involved in antigen presentation and T cell activation, we suggest that neutrophils in Atlantic salmon have potential to function as professional APCs. This work makes an important basis for further exploring the potential of using neutrophils to develop new, targeted immunoprophylactic measures. [ABSTRACT FROM AUTHOR]

The study of immunostimulant derived from natural sources has received considerable attention in recent years. Indonesian coasts have various sources of immunostimulant, especially brown algae, which are rich in alginate. This research investigated innate immune response and immune genes in red tilapia (Oreochromis sp.) after being fed diets supplemented with sodium alginates (SA) from a brown alga, Padina australis, originating from Awur Bay, Jepara, Indonesia. This work provided comprehensive information regarding the interaction of cellular-humoral immunity and immune gene expression. Red tilapia was fed with SA-containing diet at doses of 0, 2, 3 and 4 g/kg for 12 days, then blood samples were collected on days 0, 3, 6, 9, and 12 to evaluate the total leucocyte count (TLC), phagocytic activity/index (PA/PI), respiratory burst, superoxide dismutase (SOD), lysozyme, alternative complement (ACH50) activity, total plasma protein (TPP), and immune genes expression (blood sample on day 6). The immunological parameters improved in response to the administered doses and period. Dietary SA enhanced total leucocyte count, phagocytic activity, respiratory burst, superoxide dismutase, lysozyme, and ACH50 activity, whereas the phagocytic index and total plasma protein were not significantly different. Furthermore, the mRNA levels of antioxidant-related gene (GPx), proinflammatory cytokines (TNF-α and IFN-γ, except for IL-1ß), and antimicrobial peptides (Hepcidin) were upregulated. Meanwhile, anti-inflammatory cytokines (IL-10 and TGF-ß1) were downregulated. Supplementation SA diet at 2.0 g/kg as the lowest dose revealed the most effective effects on innate immune and immune genes expression. Dietary SA was a potential immunostimulant in red tilapia aquaculture. [ABSTRACT FROM AUTHOR]

The vital goal of aquaculture genomics, genetics and genomic editing is to enhance production efficiency in aquaculture sector. Rainbow trout (RBT) Oncorhynchus mykiss is a native species from the northwest coast of North America and it belongs to salmonid family. Rainbow trout is an important species in, wild stock fisheries and recreational sport fisheries in Aquaculture sector and RBT is valued for superior growth. Muscle is a molecular motor and muscle mass of livestock is crucial in food industry. Some studies reported the non-coding RNAs gene expression in muscle tissues of healthy and unhealthy (affected by muscle deterioration and muscle atrophy) fishes. During vitellogenesis, significant loss of muscle mass and sufficient muscle proteins accumulate in developing ova. This change throws a glimpse on general pattern of muscle wastage supporting RBT as an ideal model to illuminate muscle catabolism molecular mechanism. This review reports the differentially expression of microRNAs and lncRNAs of rainbow trout muscle tissues in the healthy and unhealthy fishes. [ABSTRACT FROM AUTHOR]

As an important seedling source, monospores closely associate with yields in nori farming. However, the molecular mechanism underlying differences in monospore production for different strains remains unknown. Comparative transcriptome analysis was performed to examine gene expression differences between the spore abundant wild-type strain (WT) and spore deficient mutant (Y1) of Pyropia chauhanii. The WT strain that produces monospores in abundance exhibited more differentially expressed genes (DEGs) in both number and higher fold-changes than the Y1 strain incapable of producing monospores, indicating that the specific regulation of genes is involved in monospore production. Three lists of DEGs were obtained between the two strains using intersection and displayed in Venn diagram: one expressed only in WT strain, another expressed only in Y1 strain, and the third shared in both strains. DEGs annotated as homologous genes of Arabidopsis thaliana in these 3 lists were curated for online functional enrichment analysis on Metascape website. Gene regulatory networks of WT were functionally enriched in the processing, proteolysis, and transport of proteins, especially within the small GTPase protein family, which might be account for the monospore production ability, whereas Y1 were functionally enriched in the metabolism of essential substance and utilization of indispensable energy, which might be account for the rapid growth of blades. We found the differentially enriched gene regulatory networks between strains might be the intrinsic mechanisms of the different monospore production traits. These findings provide novel insights into the genes and regulatory networks associated with monospore production abilities, which are essential for developing accurate breeding technologies for optimal release of monospores and increase of total nori production. [ABSTRACT FROM AUTHOR]

Suitable reference genes are one of the necessary conditions for obtaining reliable results by real-time fluorescence quantitative PCR (qPCR). In this study, the expression of the 10 common candidate reference genes (18s rRNA, rps27, cnbp, rpl7, ube2, hsp-at, gapdh, β-actin, rpl13a, 1-ef1a) at different developmental stages of gonad and embryo of Takifugu bimaculatus were analyzed by qPCR. And the expression stability of these reference genes is analyzed by GeNorm, NormFinder and Bestkeeper softwares. The results showed that the expression stability of 1-ef1a was the highest (p < 0.05) combined with the results of three analysis softwares, and the optimal number of reference genes was 3, which were 1-ef1a, hsp-at and rps27. Based on this result, we analyzed the expression of objective genes (foxl2 and dmrt1) at different developmental stages (early, medium-term and late) of gonads and embryos (eye vesicle stage, motility stage, heart anlage stage, retinal pigmentation stage, newly hatched larva) of T. bimaculatus by qPCR. Among which the highest expression level of foxl2 was in the middle stage of ovary (p < 0.05), and dmrt1 was expressed in the early stage of testis with the highest level (p < 0.05). The expression levels of foxl2 and dmrt1 in the early stages of embryonic development were low or even almost non-existent, and had a slight increase in the late embryonic development (newly hatched larva). The expression profile of objective genes are consistent with their roles in the development of gonads and embryos, which indicates that 1-ef1a, hspat and rps27 are the suitable reference gene combination for detecting the expression of objective genes by qPCR in gonads and embryos of T. bimaculatus. This research also provides the reliability data for screening the reference genes by qPCR in fish. [ABSTRACT FROM AUTHOR]

Heat shock proteins (HSPs) as stress-related factors play a fundamental role in innate and adaptive immune responses in fish, which can be considered as strong candidates for the development of new methods for fish disease prevention. It has been proven that Pro-Tex® as a heat shock protein inducer (HSPi) reduces harmful effects of cellular stress by increasing the Hsp70 protein production. We evaluated the effects of Pro-Tex® as an HSPi in a Persian sturgeon, (Acipenser persicus) exposed to a pathogenic bacterium. Therefore, A. persicus fries were pre-treated with 25.00, 50.00 and 100 mg L-1 of Pro-Tex® and then, injected with Streptococcus iniae ATCC29178. The Hsp70 gene expressions were determined in various organs including liver, gill and intestine and lysozyme (LYZ) activities along with supplemental levels of complement component 3 (C3) and immunoglobulin M (IgM) were also determined in sturgeon blood in days 3 and 7 after infection. Expression of Hsp70 gene was increased during the first three days of infection and then, it was found to be down-regulated during the infection process. Also, levels of LYZ activity, C3 and IgM increased in a concentration-dependent manner; but these parameters decreased after 7 days. Our data suggest that induction of Hsp70 is a promising approach in modulation of immune response in A. persicus and it might be employed to confer protection in fish against bacterial infections. [ABSTRACT FROM AUTHOR]

The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Desert ponds and coastal lagoons, located respectively upstream and at the mouths of dry riverbeds ("wadies"), have been found to potentially become connected during periods of intense rainfall, which could allow the fish to migrate between these different habitats. Flash floods would therefore flush Arabian pupfish out to sea, requiring a rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 h to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodelling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats. [ABSTRACT FROM AUTHOR]

An 8-week growth trial was conducted to examine the efficacy of pineapple peel powder (PAPP) on growth rate and immunity of Nile tilapia, O. niloticus. Three hundred Nile tilapia (20.91 ± 0.11 g) were fed five diets containing different levels of PAPP at 0, 10, 20, 30 and 40 g kg−1 PAPP, respectively. After four and eight weeks of the feeding trial, growth rates, and immune responses were tested. A challenge test using Streptococcus agalactiae and relative immune gene expression were performed after eight weeks of PAPP feeding. It was found that skin mucus and serum lysozyme, skin mucus and serum peroxidase, alternative complement, phagocytosis, and respiratory burst activities were significantly increased with the addition of PAPP. The maximum (P ≤ 0.05) innate immune values were noted in fish fed 10 g kg−1 PAPP. Similarly, the up-regulation of IL1, IL8 , and LBP gene expressions were also detected in fish fed PAPP diets, with the maximum value was found in 10 g kg−1 PAPP fed fish. The relative percentage of survival (RPS) of Oreochromis niloticus after the challenge test were (56.00%, 72.00%, 60.00%, and 44.00%) for the 5, 10, 20 and 40 g kg−1 PAPP diets, respectively. Fish fed the 10 g kg−1 PAPP supplemented diet achieved the highest (P < 0.05) survival rate against S. agalactiae. Growth and feed efficiency were outstandingly (P < 0.05) enhanced in the PAPP groups. In conclusion, PAPP can be potentially used as a feed additive in Nile tilapia culture under Biofloc system. • Fish fed 10 g kg−1 PAPP showed significant increase in mucosal and serum immune response. • Up-regulation of IL-1, IL-8, and LBP Nile tilapia live was observed in fish fed 10 g kg−1 PAPP. • g kg−1 PAPP significantly increased survival rate of O. niloticus against S. agalactiae. • Nile tilapia fed 10 g kg−1 PAPP significantly improved growth performance and FCR. [ABSTRACT FROM AUTHOR]

This study was carried out to investigate the ameliorating effect of dietary curcumin Curcuma longa (CUR) against the subacute toxicity of fipronil (FIP) on Oreochromis niloticus. One hundred and eighty fish were divided into six groups and kept for 30 days; the first group was kept as a control group fed on commercial diet, while the second and third groups were fed on commercial diets supplemented with 1% (CUR1) and 3% (CUR3) curcumin powder/kg diet respectively. The fourth (FIP), fifth (FIP1) and sixth (FIP3) experimental groups were intoxicated with FIP (1/10 96 h LC50), where (FIP1) and (FIP3) groups were fed on a commercial diet supplemented with 1% and 3% of curcumin powder respectively. Hepatorenal damage markers, immunological, tissue antioxidant parameters and anterior kidney expression of IL‐8, IL‐1β and TGF‐β1 genes were determined. Curcumin alleviated the deteriorative effects of FIP intoxication through decreasing hepatic and renal damage markers, improving serum respiratory burst and lysozyme activities. Curcumin provoked a marked decrease in hepatic and renal malondialdehyde and nitric oxide concentration with a significant improvement in tissues' antioxidant status in FIP‐intoxicated fish. Gene expression analysis revealed a significant down‐expression of pro‐inflammatory markers genes after supplementation of curcumin in FIP‐intoxicated fish. In conclusion, the use of 3% curcumin as a feed additive could be implemented to protect fish against the toxic effects of agrochemical wastes via restoring antioxidant and immunological parameters of intoxicated fish. [ABSTRACT FROM AUTHOR]

Background: Hybridization, which can quickly merge two or more divergent genomes and form new allopolyploids, is an important technique in fish genetic breeding. However, the merged subgenomes must adjust and coexist with one another in a single nucleus, which may cause subgenome interaction and dominance at the gene expression level and has been observed in some allopolyploid plants. In our previous studies, newly formed allodiploid hybrid fish derived from herbivorous Megalobrama amblycephala (♀) × carnivorous Culter alburnus (♂) had herbivorous characteristic. It is thus interesting to further characterize whether the subgenome interaction and dominance derive dietary adaptation of this hybrid fish. Results: Differential expression, homoeolog expression silencing and bias were investigated in the hybrid fish after 70 days of adaptation to carnivorous and herbivorous diets. A total of 2.65 × 108 clean reads (74.06 Gb) from the liver and intestinal transcriptomes were mapped to the two parent genomes based on specific SNPs. A total of 2538 and 4385 differentially expressed homoeologous genes (DEHs) were identified in the liver and intestinal tissues between the two groups of fish, respectively, and these DEHs were highly enriched in fat digestion and carbon metabolism, amino acid metabolism and steroid biosynthesis. Furthermore, subgenome dominance were observed in tissues, with paternal subgenome was more dominant than maternal subgenome. Moreover, subgenome expression dominance controlled functional pathways in metabolism, disease, cellular processes, environment and genetic information processing during the two dietary adaptation processes. In addition, few but sturdy villi in the intestine, significant fat accumulation and a higher concentration of malondialdehyde in the liver were observed in fish fed carnivorous diet compared with fish fed herbivorous diet. Conclusions: Our results indicated that diet drives phenotypic and genetic variation, and the asymmetric expression of homoeologous genes (including differential expression, expression silencing and bias) may play key roles in dietary adaptation of hybrid fish. Subgenome expression dominance may contribute to uncovering the mechanistic basis of heterosis and also provide perspectives for fish genetic breeding and application. [ABSTRACT FROM AUTHOR]

Diseases outbreak caused by pathogenic organisms is known to be one of the significant constraints faced by fish farmers and consequently pose great damage to the economy of the aquaculture sector. Vaccines and antibiotics are used to prevent the spreading of infectious diseases. However, these practices are cost‐ineffective and may increase the resistance of pathogens towards antibiotics. Therefore, the use of immunostimulants in aquaculture as an alternative to antibiotics and vaccines is becoming popular nowadays. The selection of a suitable and effective immunostimulant for fish is essential to protect them against the pathogens. β‐glucan, a potent immunostimulant, is widely used in aquaculture to improve the immune system of fish. β‐glucan is a highly conserved carbohydrate that can be found in the cell wall of yeast, fungi, plant and even some bacteria species. The immunomodulatory role of β‐glucans on fish immunity are well identified in aquaculture research, whereby it was mainly investigated through the regulation of cellular and humoural immune parameters, immune‐related genes and proteins expression, and resistance towards various infectious diseases. This review summarizes the recent literature on the mode of action of β‐glucans in fish immunity via a different route of administration. The suitable dose, duration and frequency of β‐glucans administration for optimal stimulation in different species of fish, as well as the combinational used of β‐glucans with one or more immunostimulants, were also highlighted. [ABSTRACT FROM AUTHOR]

Edwardsiella piscicida (E. piscicida) is an important fish pathogen. However, the mechanism of Glu6P transport regulatory protein UhpA how to affect the virulence gene expression in E. piscicida is still unclear. The results in this study showed that the metabolism‐related gene expression of cysteine synthase (orf 1134) and sulphate transporter (ychM) in the uhpA mutant strain ΔuhpA was 0.76‐fold and 0.68‐fold lower than the ones in the wild strains (p <.05). The gene expression of ethA and ethB in the ΔuhpA strain was 0.80‐fold and 0.72‐fold lower than the ones in the wild strains (p <.05). However, the gene expression of fliC and flgN in the ΔuhpA was 1.51‐fold and 1.21‐fold higher than the ones in the wild strains (p <.05). The gene expression of T3SS (esrB and esrC) and T6SS (evpB and evpC) in the ΔuhpA was 1.27‐fold, 1.13‐fold, 1.28‐fold and 1.23‐fold higher than the ones in the wild strains (p <.05). This suggested that the uhpA gene could regulate the key virulence gene expression, and the uhpA gene was associated with the pathogenicity of E. piscicida in fish. [ABSTRACT FROM AUTHOR]

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Facultative migration occurs when, in response to prevailing conditions, individuals in a population may (or may not) undertake a migration. The brown trout (Salmo trutta) is a species that exhibits facultative migration, where some individuals within populations may move to mainstem rivers (fluvial–adfluvial migration), lakes (lacustrine–adfluvial migration), estuaries (partial anadromy) or sea (anadromy) to feed, while others remain resident. This study attempts to separate two alternative hypotheses for the population structuring that underpins the expression of facultative migration in this species: (a) that anadromous and nonanadromous fish comprise two gene pools; (b) that individual genetic variation or individual variation in gene–environment interactions is responsible for the expression of different life‐history tactics within the same gene pool. The study design involved sampling and analyses of anadromous and nonanadromous brown trout from three independent tributary rivers known to produce (sea‐run) trout within the same catchment. Results indicate that, in all cases, population genetic divergence was linked to geographical location and not to life‐history tactics. Two genetically distinct coexisting population pairs were identified in two separate tributaries. Despite similar environmental conditions in both tributaries, the frequency of each life‐history tactic (anadromy vs. nonanadromous) within these population pairs differed significantly. The results of this study support the hypothesis that facultative migration in brown trout is likely to be driven by a quantitative threshold trait, where the threshold value varies both among populations and among individuals within populations. [ABSTRACT FROM AUTHOR]

Circadian clock genes are crucial for generating and sustaining most rhythmic daily functions in the animal kingdom, which entrain the rhythms of biochemical, physiological, and behavioural processes. To better understand the molecular oscillations of the circadian rhythms in darkbarbel catfish (Pelteobagrus vachellii), we isolated and characterized two circadian clock genes in P. vachellii, period 1 (per1), and period 3 (per3). The circadian clock gene per1 was found to encode a 1 428-amino acid polypeptide, including PER-ARNT-SIM (PAS) dimerisation domains, a PAS-associated C-terminal motif (PAC), a short mutable domain (S/M), and a nuclear export signal (NES). The 4 902-bp per3 cDNA includes an open reading frame encoding a 1 292-amino acid residue polypeptide with a PER-ARNT-SIM (PAS) domain, cytoplasmic localisation domain (CLD), interaction site (TIS), and a nuclear localisation signal (NLS). The per1 and per3 gene was constitutively expressed in all examined tissues. Moreover, per1 expression within a light/dark cycles showed rhythmic expression in the diencephalon, brain, liver and intestine, with the acrophase at 15:15, 12:52, 7:51, and 12:55, respectively. Daily expression of per3 was rhythmic in the diencephalon, brain, liver and intestine, with the acrophase at 8:15, 9:54, 10:39, and 10:25 h, respectively. These findings expand our understanding of circadian mechanism at the molecular level in this species. [ABSTRACT FROM AUTHOR]

Diseases caused by myxozoan parasites represent a significant threat to the health of salmonids in both the wild and aquaculture setting, and there are no effective therapeutants for their control. The myxozoan Ceratonova shasta is an intestinal parasite of salmonids that causes severe enteronecrosis and mortality. Most fish populations appear genetically fixed as resistant or susceptible to the parasite, offering an attractive model system for studying the immune response to myxozoans. We hypothesized that early recognition of the parasite is a critical factor driving resistance and that susceptible fish would have a delayed immune response. RNA-seq was used to identify genes that were differentially expressed in the gills and intestine during the early stages of C. shasta infection in both resistant and susceptible steelhead (Oncorhynchus mykiss). This revealed a downregulation of genes involved in the IFN-γ signaling pathway in the gills of both phenotypes. Despite this, resistant fish quickly contained the infection and several immune genes, including two innate immune receptors were upregulated. Susceptible fish, on the other hand, failed to control parasite proliferation and had no discernible immune response to the parasite, including a near-complete lack of differential gene expression in the intestine. Further sequencing of intestinal samples from susceptible fish during the middle and late stages of infection showed a vigorous yet ineffective immune response driven by IFN-γ, and massive differential expression of genes involved in cell adhesion and the extracellular matrix, which coincided with the breakdown of the intestinal structure. Our results suggest that the parasite may be suppressing the host's immune system during the initial invasion, and that susceptible fish are unable to recognize the parasite invading the intestine or mount an effective immune response. These findings improve our understanding of myxozoan-host interactions while providing a set of putative resistance markers for future studies. [ABSTRACT FROM AUTHOR]

Gamma radiation produces DNA instability and impaired phenotype. Previously, we observed negative effects on phenotype, DNA methylation, and gene expression profiles, in offspring of zebrafish exposed to gamma radiation during gametogenesis. We hypothesize that previously observed effects are accompanied with changes in the expression profile of non-coding RNAs, inherited by next generations. Non-coding RNA expression profile was analysed in F1 offspring (5.5 h post-fertilization) by high-throughput sequencing 1 year after parental irradiation (8.7 mGy/h, 5.2 Gy total dose). Using our previous F1-γ genome-wide gene expression data (GSE98539), hundreds of mRNAs were predicted as targets of differentially expressed (DE) miRNAs, involved in pathways such as insulin receptor, NFkB and PTEN signalling, linking to apoptosis and cancer. snRNAs belonging to the five major spliceosomal snRNAs were down-regulated in the F1-γ group, Indicating transcriptional and post-transcriptional alterations. In addition, DEpiRNA clusters were associated to 9 transposable elements (TEs) (LTR, LINE, and TIR) (p = 0.0024), probable as a response to the activation of these TEs. Moreover, the expression of the lincRNAs malat-1, and several others was altered in the offspring F1, in concordance with previously observed phenotypical alterations. In conclusion, our results demonstrate diverse gamma radiation-induced alterations in the ncRNA profiles of F1 offspring observable 1 year after parental irradiation. [ABSTRACT FROM AUTHOR]

The rapid growth of production in aquaculture in the last decades has brought unwanted consequences affecting fish health and increasing the susceptibility to different infections. This systematic review aimed to analyse and summarize the current knowledge of gene expression responses to infectious diseases in teleosts using viruses, bacteria, fungi and parasites as agents through published microarray data. We conducted searches in electronic databases, including PubMed, Web of Science and SCOPUS until 1 May 2019. We identified 862 citations across databases and manual searches. After removing duplicates, we screened 455 unique references using titles and abstracts, of which 262 proved potentially eligible and evaluated using full text. A total of 79 articles proved eligible for this review. From the articles retrieved, we examined 261 different experiments (or 'studies') and more than a hundred thousand differentially expressed genes (DEGs). This systematic review represents the first catalogue of genes (and their associated processes) that differentially transcribe in different teleost species (13 species) due to infections generated by a large variety of pathogens (38 types). Although the obtained gene expression results are in considerable measure associated with expected immune response, other genes showed surprising significant transcriptional outcomes that may unravel unknown functions related to fish infections. This type of investigations facilitates the visualization of existing gaps in researches that may inspire future analysis in non‐traditional but relevant host or pathogen species. [ABSTRACT FROM AUTHOR]

Genetic selection of disease resistant fish is a major strategy to improve health, welfare and sustainability in aquaculture. Mapping of single nucleotide polymorphisms (SNP) in the fish genome may be a fruitful tool to define relevant quantitative trait loci (QTL) and we here show its use for characterization of Vibrio anguillarum resistant rainbow trout (Oncorhynchus mykiss). Fingerlings were exposed to the pathogen V. anguillarum serotype O1 in a solution of 1.5 × 107 cfu/ml and observed for 14 days. Disease signs appeared 3 days post exposure (dpe) whereafter mortality progressed exponentially until 6 dpe reaching a total mortality of 55% within 11 days. DNA was sampled from all fish – including survivors – and analyzed on a 57 k Affymetrix SNP platform whereby it was shown that disease resistance was associated with a major QTL on chromosome 21 (Omy 21). Gene expression analyses showed that diseased fish activated genes associated with innate and adaptive immune responses. The possible genes associated with resistance are discussed. [ABSTRACT FROM AUTHOR]

Galectin-8 and galectin-9 belong to tandem repeat-type galectins, and in the present study, these two genes were cloned in mandarin fish Siniperca chuatsi. The open reading frame (ORF) of the mandarin fish galectin-8 and galectin-9 contains 942, and 1008 bp, encoding 313 and 335 amino acids, respectively. As a conserved feature, an N-terminal carbohydrate recognition domain (CRD), and a C-terminal CRD were observed in each of the two galectins in mandarin fish. In healthy fish, galectin-8 and -9 were constitutively expressed in all organs/tissues examined, and their expression can be induced following the stimulation of LPS and poly(I:C). It is obvious that galectin-8 had a higher increase at mRNA level following the stimulation of poly(I:C). It is further demonstrated that mandarin fish galectin-8 inhibited the growth of Flavobacterium columnare and Streptococcus agalactiae , and in addition to the two species of bacteria, galectin-9 inhibited also the growth of Edwardsiella piscicida , which provides the basis for further understanding their antibacterial role in immune response of mandarin fish. • Galectin-8 and galectin-9 genes were cloned from mandarin fish Siniperca chuatsi. • N-terminal carbohydrate recognition domain (CRD), and C-terminal CRD were observed in these two galectins. • Galectin-8 and -9 were constitutively expressed in all organs/tissues examined. • The expression of galectin-8 and -9 were induced following LPS and also poly(I:C) stimulation. • Galectin-8 and galectin-9 inhibited the growth of F. columnare and S. agalactiae. [ABSTRACT FROM AUTHOR]

Organic acids (OA) and nature-identical compounds (NIC) such as monoterpenes and aldehydes are well-known growth and health promoters in terrestrial livestock while their application for fish production is recent and their mechanisms of action require further study. Hence, this study tested the increasing dietary level (D0, D250, D500, D1000; 0, 250, 500 and 1000 mg kg feed−1 respectively) of a microencapsulated blend containing citric and sorbic acid, thymol and vanillin over 82 days on rainbow trout to assess the effects on growth, feed utilization, intestine cytokine gene expression and gut microbiota (GM). Furthermore, the effects on intestinal cytokine gene expression and GM were also explored after one week at high water temperature (23 °C). OA and NIC improved specific growth rate (SGR) and feed conversion rate (FCR) during the second half (day 40–82) of the feeding trial, while at the end of the trial protein (PER) and lipid efficiency (LER) increased with increasing dietary level. GM diversity and composition and cytokine gene expression analysis showed no significant differences in fish fed with increasing doses of OA and NIC (82 days) demonstrating the absence of inflammatory activity in the intestinal mucosa. Although there were no statistical differences, GM structure showed a tendency in clustering D0 group separately from the other dietary groups and a trend towards reduction of Streptococcus spp. was observed in the D250 and D1000 groups. After exposure to high water temperature, lower GM diversity and increased gene expression of inflammatory intestinal cytokines were observed for both inclusions (D0 vs. D1000) compared to groups in standard condition. However, the gene up-regulation involved a limited number of cytokines showing the absence of a substantial inflammation process able to compromise the functional activity of the intestine. Despite further study should be conducted to fully clarify this mechanism, cytokines up-regulation seems to be concomitant to the reduction of the GM diversity and, particularly, to the reduction of specific lactic acid bacteria such as Leuconostoc. The application of the microencapsulate blend tested can be a useful strategy to improve growth and feed utilization in rainbow trout under normal temperature conditions. According to the results organic acids and nature-identical compounds did not revert the effects triggered by the increased temperature of water. • Dietary organic acid and nature-identical compounds improved growth in rainbow trout. • No diet effect was observed on intestinal cytokines expression and gut microbiome. • High water temperature up-regulated cytokines and reduced microbiome diversity. • Diets did not revert the effects triggered by the increased temperature of water. [ABSTRACT FROM AUTHOR]

The aquatic environment is massively polluted with endocrine-disrupting compounds (EDCs) including synthetic estrogens (e.g. 17α-ethinylestradiol, EE2) and alkylphenols (e.g. 4- tert- octylphenol, 4 t -OP). A major mechanism of action for estrogenic EDCs is their interaction with estrogen receptors and consequently their modulation of the action of enzymes involved in steroid conversion e.g. aromatase CYP19. We now studied the effects of EE2 and 4 t -OP on the anti-bacterial immune response of common carp. We investigated effects on the number/composition of inflammatory leukocytes and on the gene expression of mediators that regulate inflammation and EDC binding. In vitro we found that high concentrations of both EE2 and 4 t -OP down-regulated IFN-γ2 and IFN-γ-dependent immune responses in LPS-stimulated monocytes/macrophages. Similarly, during bacterial infection in fish, in vivo treated with EE2 and 4 t -OP, decreased gene expression of il-12p35 and of ifn-γ2 was found in the focus of inflammation. Moreover, during A. salmonicida -induced infection in EE2-treated carp, but not in fish fed with 4 t -OP-treated food, we found an enhanced inflammatory reaction manifested by high number of inflammatory peritoneal leukocytes, including phagocytes and higher expression of pro-inflammatory mediators (inos, il-1β, cxcl8_l2). Furthermore, in the liver, EE2 down-regulated the expression of acute phase proteins: CRPs and C3. Importantly, both in vitro and in vivo , EDCs altered the expression of estrogen receptors: nuclear (erα and erβ) and membrane (gpr30). EDCs also induced up-regulation of the cyp19b gene. Our findings reveal that contamination of the aquatic milieu with estrogenic EDCs, may considerably violate the subtle and particular allostatic interactions between the immune response and endogenous estrogens and this may have negative consequences for fish health. • High concentration of EE2 and 4t-OP down-regulate in vitro IFN-γ-dependent immune responses. • During bacterial infection in EE2 in vivo enhances inflammatory reaction. • Water contamination with estrogenic EDCs have negative consequences for fish health. [ABSTRACT FROM AUTHOR]

The fish hydrolyzed protein is the potential source of bioactive peptides. These peptides are inactive in the original structure of the protein molecule, but they can be activated after enzymatic hydrolysis. In this research, the effect of the half maximal inhibitory concentration (IC50) rainbow trout hydrolyzed proteins (< 3 kDa) was evaluated on enterotoxin A gene expression of Staphylococcus aureus ATCC 29,213 (the strain of enterotoxin A producer). After affecting IC50 of the fish hydrolyzed protein (< 3 kDa) and S. aureus 1.5 × 108 cfu/ml in BHI broth medium and incubating for the durations 8 and 12 h after exposure (logarithmic phase and stationary phase of S. aureus growth, respectively), the gene expression of enterotoxin A was investigated via Real-Time PCR. gyrA used as a housekeeping endogenous control. Notably only < 3 kDa fish hydrolyzed protein by Flavourzyme enzyme (HF3) showed an inhibitory effect on gene expression of S. aureus enterotoxin A in logarithmic phase. Therefore, fish hydrolyzed proteins can provide a new strategy as natural factors in preventing toxin production, due to the high quality and safety of sensitive foods. [ABSTRACT FROM AUTHOR]

Many parasites with complex life cycles modify their intermediate hosts' behaviour, presumably to increase transmission to their final host. The threespine stickleback (Gasterosteus aculeatus) is an intermediate host in the cestode Schistocephalus solidus life cycle, which ends in an avian host, and shows increased risky behaviours when infected. We studied brain gene expression profiles of sticklebacks infected with S. solidus to determine the proximal causes of these behavioural alterations. We show that infected fish have altered expression levels in genes involved in the inositol pathway. We thus tested the functional implication of this pathway and successfully rescued normal behaviours in infected sticklebacks using lithium exposure. We also show that exposed but uninfected fish have a distinct gene expression profile from both infected fish and control individuals, allowing us to separate gene activity related to parasite exposure from consequences of a successful infection. Finally, we find that selective serotonin reuptake inhibitor-treated sticklebacks and infected fish do not have similarly altered gene expression, despite their comparable behaviours, suggesting that the serotonin pathway is probably not the main driver of phenotypic changes in infected sticklebacks. Taken together, our results allow us to predict that if S. solidus directly manipulates its host, it could target the inositol pathway. [ABSTRACT FROM AUTHOR]

This study assessed the impact of routine vaccination of Atlantic salmon pre-smolts on gene expression and the possible link to saprolegniosis on Scottish fish farms. Fish were in 4 different groups 1) 'control' – fish without handling or vaccination 2) 'vaccinated' - fish undergoing full vaccination procedure 3) 'non vaccinated' - fish undergoing full vaccination procedure but not vaccinated and 4) 'vaccinated-MH' – fish undergoing vaccination, but procedure involved minimal handling. A strong increase in cortisol and glucose levels was observed after 1 h in all groups relative to the control group. Only in the non-vaccinated group did the level decrease to near control levels by 4 h. Expression levels of six stress marker genes in general for all groups showed down regulation over a 9-day sampling period. In contrast, expression levels for immune response genes in the head kidney showed significant up-regulation for all eight genes tested for both vaccinated groups whereas the non-vaccinated group showed up-regulation for only MHC-II and IL -6b in comparison to the control. Both the vaccination procedure and the administration of the vaccine itself were factors mediating changes in gene expression consistent with fish being susceptible to natural occurring saprolegniosis following vaccination. • Vaccination and handling of pre-smolt salmon trigger stress response. • Routine farm vaccinated fish, but not unvaccinated fish, become infected with Saprolegnia. • Unique stress and inflammatory gene expression changes in young vaccinated salmon. [ABSTRACT FROM AUTHOR]

This study investigated the stimulatory effects of dietary inclusion of Gracilariopsis persica (GP), Hypnea flagelliformis (HF) and Sargassum boveanum (SB) on immune indices, antioxidant capability and immune related genes expression of rainbow trout (Oncorhynchus mykiss). Seven iso-nitrogenous and iso-caloric diets with 0, 5 and 10% of each macroalgae were prepared and fed to rainbow trout juveniles for 83 days. Serum lysozyme (Lyz) and respiratory burst activity (NBT) along with activity of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) and expression of LyzII , TNFα and IL - 1β genes in head kidney samples were determined by days 47 and 83. Our results revealed that dietary inclusion of seaweeds improved fish immune status. Long term feeding of fish on seaweed contained diets (except for GP10) improved serum Lyz activity in comparison to control group. Similarly, extended feeding on GP5 and HF10 and HF10 included diets improved SOD and POD levels, respectively. Genes expression studies revealed that seaweeds contained diets noticeably enhanced expression of LyzII , TNFα and IL-1β in comparison to control fish. However, results revealed that such stimulatory effects were more evident at lower dietary inclusion level and shorter feeding time. In conclusion, the results depicted that dietary inclusion of the seaweeds effectively improved serum immune indices and head kidney antioxidant status and immune related genes expression in a time and dose dependent manner. • Dietary inclusion of three seaweeds improved rainbow trout immune status. • Long-term feeding resulted in higher immunostimulatory capacity than shorter feeding trial. • Expression of LyzII , TNFα and IL-1β genes were more influenced at lower dietary inclusion level and shorter feeding time. [ABSTRACT FROM AUTHOR]

Extracellular ATP (eATP) is a potent singling molecule in activation of fish innate immunity while the molecular determinants for eATP release in fish were not completely understood. Connexin32 (Cx32) is a member of gap junction protein family that plays important immunological functions in mammals. However, the immune relevance of Cx32 and its role in ATP release in fish has not been investigated. Here, we identified, characterized three Cx32 isoform genes (Cx32.2 , Cx32.2x and Cx32.7) from the Japanese flounder Paralichthys olivaceus , and investigated their role in inflammation-induced ATP release in fish. Expression analysis revealed that even though all the three Cx32 genes are constitutively expressed in all examined Japanese flounder tissues, Cx32.2 and Cx32.2x are dominantly expressed in liver, and Cx32.7 is highly expressed in intestine and head kidney macrophages. In addition, we showed that gene expression of all the three Cx32 isoforms was modulated by cAMP stimulation and inflammatory challenges. Furthermore, we revealed that Cx32 expression was upregulated in TNF-alpha overexpressed Japanese flounder FG-9307 cells. Moreover, overexpression of the three Cx32 isoforms significantly reduced the gene expression level of LPS-induced pro-inflammatory cytokine IL-8 and TNF-alpha , indicating that Cx32 is involved in modulating inflammatory response in fish. Finally, we showed that inflammation-induced ATP release was significantly increased in Cx32-overexpressed Japanese flounder FG-9307 cells, and this increased ATP release could be attenuated by pre-incubation with gap junction protein blocker carbenoxolone. Taken together, we for the first time reported the involvement of Cx32 in fish immunity. Our findings suggested that in addition to Cx43 and pannexin1 channels, Cx32 also plays a role in inflammation-induced ATP release in fish. • Three Cx32 isoform genes were expressed in Japanese flounder Paralichthys olivaceus. • Cx32 expression was modulated by PAMPs challenge and cAMP stimulation. • TNF-alpha overexpression up-regulated Cx32 expression. • Cx32 down-regulated LPS-induced pro-inflammatory cytokine expression. • Cx32 is an immune response gene involved in inflammation-induced ATP release in fish. [ABSTRACT FROM AUTHOR]

Selective breeding programmes involving marker assisted selection of innately pathogen resistant strains of rainbow trout rely on reliable controlled infection studies, extensive DNA typing of individual fish and recording of expression of relevant genes. We exposed juvenile rainbow trout (6 h bath to 2.6 × 105 CFU mL−1) to the fish pathogen Yersinia ruckeri serotype O1, biotype 2, eliciting Enteric Red Mouth Disease ERM, and followed the disease progression over 21 days. Cumulative mortality reached 42% at 12 days post challenge (dpc) after which no disease signs were recorded. All fish were sampled for DNA-typing (50 k SNP chip, Affymetrix®) throughout the course of infection when they showed clinical signs of disease (susceptible fish) or at day 21 when fish showed no clinical signs of disease (survivors - resistant fish). Genome-wide association analyses of 1027 trout applying single nucleotide polymorphisms (SNPs) as markers revealed an association between traits (susceptible/resistant) and certain regions of the trout genome. It was indicated that multiple genes are involved in rainbow trout resistance towards ERM whereby it is considered a polygenic trait. A corresponding trout group was kept as non-exposed controls and a comparative expression analysis of central innate and adaptive immune genes in gills, spleen and liver was performed for three fish groups: 1) moribund trout exhibiting clinical signs 7 dpc (CS), 2) exposed fish without clinical signs at the same sampling point (NCS) and 3) surviving fish at 21 dpc (survivors). Immune genes encoding inflammatory cytokines (IL-1β, IL-2A, IL-6A, IL-8, IL-10A, IL-12, IL-17A/F2A, IL-17C1, IL-17C2, IL-22, IFNγ, TNFα), acute phase reactants (SAA, C3, cathelicidins, lysozyme) were expressed differently in CS and NCS fish. Correlation (negative or positive) between expression of genes and bacterial load suggested involvement of immune genes in protection. Down-regulation of adaptive immune genes including IgDm, IgDs, IgT and TCR-β was seen primarily in CS and NCS fish whereas survivors showed up-regulation of effector molecule genes such as cathelicidins, complement and lysozyme suggesting their role in clearing the infection. In conclusion, SNP analyses indicated that ERM resistance in rainbow trout is a multi-locus trait. The gene expression in surviving fish suggested that several immune genes are associated with the trait conferring resistance. • SNP analyses of rainbow trout indicated that resistance against Yersinia ruckeri is a polygenic trait. • Expression of immune relevant genes different significantly between resistant and susceptible trout. • Trout surviving the infection exhibited upregulated genes encoding innate effector molecules. [ABSTRACT FROM AUTHOR]

Monogenean Gyrodactylus cichlidarum can cause severe mortality of Nile tilapia (Oreochromis niloticus) fry. To date, reports about mucosal immunity of O. niloticus against this parasite have been rare. In order to explore the mucosal immunity of Nile tilapia against G. cichlidarum infection, the expressions of six adaptive immune-related genes and the contents of specific immunoglobulin IgM and IgT in the skin-associated lymphoid tissues (SALT) were dynamically analyzed after primary and secondary infections. The abundances of G. cichlidarum on the hosts after secondary infection were lower than those after primary parasite infection, which implied that hosts could initiate immune protection against G. cichlidarum reinfection to some degree. The transcription levels of TCR-β and CD4 genes in the skin tissue were significantly up-regulated after primary G. cichlidarum infection, while genes pIgR and IgT were only detected with significant up-regulations during secondary infection. With the exception of pIgR, which had remarkably higher expression in the fish with low parasite loads, all other genes studied tended to have higher mRNA level in the fish with higher parasite loads. The specific IgM content in the skin mucus increased significantly on the 2nd day after the primary exposure, higher than the corresponding value during the secondary exposure, and had significantly positive correlation with the parasite loads during the first parasite infection. These results manifested that acquired immune responses in the SALT of Nile tilapia participated in the resistance against G. cichlidarum infection, underscoring the involvement of mucosal immunity in fish against monogenean infection, and suggesting potential prophylactic treatment of gyrodactylid disease of tilapia. • G. cichlidarum loads in reinfection were lower than those in primary infection. • Significant up-regulations of adaptive immune-related genes expressions were detected. • Specific IgM significantly increased and had positive correlation with parasite loads. [ABSTRACT FROM AUTHOR]

Extreme environments often result in the evolution of dramatic adaptive features. The Mexican tetra, Astyanax mexicanus, includes 30 different populations of cave‐dwelling forms that live in perpetual darkness. As a consequence, many populations have evolved eye loss, reduced pigmentation, and amplification of nonvisual sensory systems. Closely‐related surface‐dwelling morphs demonstrate typical vision, pigmentation, and sensation. Transcriptomic assessments in this system have revealed important developmental changes associated with the cave morph, however, they have not accounted for photic rearing conditions. Prior studies reared individuals under a 12:12 hr light/dark (LD) cycle. Here, we reared cavefish under constant darkness (DD) for 5+ years. From these experimental individuals, we performed mRNA sequencing and compared gene expression of surface fish reared under LD conditions to cavefish reared under DD conditions to identify photic‐dependent gene expression differences. Gene Ontology enrichment analyses revealed a number of previously underappreciated cave‐associated changes impacting blood physiology and olfaction. We further evaluated the position of differentially expressed genes relative to QTL positions from prior studies and found several candidate genes associated with these ecologically relevant lighting conditions. In sum, this work highlights photic conditions as a key environmental factor impacting gene expression patterns in blind cave‐dwelling fish. Research Highlights: This transcriptomic study examines gene expression changes in obligate cave dwelling animals when reared under different photic conditions.Many physiological systems are impacted by light, including olfaction and blood physiology. [ABSTRACT FROM AUTHOR]

Tumor necrosis factor superfamily (TNFSF) molecules are important inflammatory cytokines, which are involved in diverse immunological functions such as B-cell regulation and B-cell-mediated immune responses. Existence of numerous tumor necrosis factor (TNF) members in the evolutionary lower vertebrate species has been reported; however, their immune functions are yet to be explored. Therefore, the existence of TNFSF members such as B-cell activating factor (BAFF) and a proliferation-inducing ligand (APRIL) were identified in the freshwater carp, Catla catla. The BAFF and APRIL of C. catla (CcBAFF) and (CcAPRIL) were confirmed with the help of bioinformatic analysis. The CcBAFF showed higher structural identity with the BAFF of Xenopus laevis (amphibian) and BAFF-human. Further, the phylogenetic analysis ensured the conserved sequence similar to that of other teleosts. CcBAFF protein sequence had a predicted transmembrane domain and a typical TNF homology domain. CcBAFF and CcAPRIL were found to be constitutively expressed in all the immunological tissues. Spleen and gill had shown an elevated expression compared with other tissues in all the infected/stimulated (bacterial, viral antigen, and parasitic) fish. Stimulation by ligands (Poly I:C, LPS, PGN, and FLA) in C. catla had shown an elevation in the expression of CcBAFF and CcAPRIL in spleen and gill at different time intervals. The expression of recombinant CcBAFF has been confirmed with the immunoblotting. Thus, this is the first report that indicates the presence of BAFF and APRIL in Catla catla and its potential role in immunity. [ABSTRACT FROM AUTHOR]

The present study investigated the possible effects of including salt of short chain fatty acid, sodium acetate (SA), on skin mucus immune parameters and immune, antioxidant and growth-related genes expression in common carp. There is little data available about the effective role of SA on immune, antioxidant and growth related genes expression as well as skin mucus immune parameters. The aim of this study was to analyse the effect of SA intake on these factors using common carp (Cyprinus carpio) as model organism. Two hundred and forty healthy common carps (mean weight = 15 ± 0.9 g) were supplied and randomly stocked into 12 fiberglass tanks 200 L (20 fish per tank) assigned to four treatments and triplicates. The study was performed in a completely randomized design. The treatments were feeding carps with experimental diets containing different levels (0.0 [control], 0.5, 1 and 2%) of SA. The skin mucus total immunoglobulin and total protein levels in fish fed 2% SA showed significant increase compared to the control group (P<0.05). Results showed a significant increase in the GH gene expression in 1 and 2% SA treatments (P<0.05). The carps fed the diet with 2% SA showed a significant increase in IGF-1 expression (P<0.05). The expression of GSTa, and GPX (antioxidant genes) revealed a significant increase in the GSTa (fish fed SA at 1% and 2% levels) and GPX gene expression with fish fed 2% SA (P<0.05). Supplementation of fish diet with SA induced a slight elevation in the intestine of all immune-related genes (TNF-α, IL-1β, IL8 and Lyz) compared to the control group (P>0.05). However, Lyz gene was significantly up-regulated in 1 or 2% SA treatments. These results confirmed beneficial effects of SA as a feed additive in common carp culture. [ABSTRACT FROM AUTHOR]

In this study, effects of nettle (Urtica dioica) on growth, immunity, and gene expressions were examined in rainbow trout after an 8-week feeding period. A total of 264 juvenile rainbow trout (10.72 ± 0.55 g) were selected and stocked randomly in 12 aquaria. Nettle powder was added to the fish feed at three doses, 0.5,1 and 1.5% served as treatments. At the end of 8-week feeding period, the fish were exposed to Saprolegnia parasitica for 3 weeks. Results showed that all treatments fed with nettle diets exhibited significant increases in weight gain and SGR, and decreased FCR compared to the control. Feeding the fish with dietary nettle resulted in significant rises in blood indices and non-specific immunity in comparison with the control. Furthermore, fish fed 0.5% of dietary nettle showed significantly increased expressions of TNF-α, IL-1b, IL-6 and IL-8 genes following 8 weeks of feeding. A significant reduction in mortality rate was observed in the fish treated with 0.5% of nettle compared to the control following challenging with S. parasitica. Our observations indicate that the use of 0.5% nettle powder in rainbow trout diet can improve growth and immunity parameters as well as fish resistance against S. parasitica contamination. • The rainbow trout fed with nettle (Urtica dioica) diets exhibited significant increases in growth parameters. • Fish fed 0.5% of dietary nettle showed significantly increased expressions of TNF-α, IL-1b, IL-6 and IL-8 genes. • Reduction in mortality was observed in the fish treated with 0.5% of nettle after challenge with Saprolegnia parasitica. [ABSTRACT FROM AUTHOR]

The Nile tilapia (Oreochromis niloticus) is one of the major food fish species produced in tropical and subtropical regions. However, this industry has been facing significant challenges from microbial infections. Understanding how hosts initiate immune responses against invading microbes is the first requirement for addressing disease outbreak prevention and disease resistance. Toll-like receptors (TLRs) are a family of evolutionarily conserved proteins that can recognize pathogen-associated molecular patterns (PAMPs). They thus play an essential role in innate immunity. TLR25 is a newly identified fish-specific member of the TLR1 subfamily. In this study, we investigate the molecular and functional characteristics of O. niloticus TLR25 (OnTLR25) via tissue expression patterns, gene expression modulation after challenge with bacteria and TLR ligands, subcellular localization in human and fish cells, and the signaling pathways TLR25 may induce. Transcriptional levels of OnTLR25 are high in immune-related organs such as the spleen and head kidney, and are increased following bacterial challenges. In addition, we show that OnTLR25 preferentially localizes to the intracellular compartment in transfected tilapia head kidney (THK) cell line. Furthermore, overexpression of the truncated form of OnTLR25 in THK cell line induced the expression of proinflammatory cytokines, such as tumor necrosis factor α , interleukin (IL) -1β , IL-8 , IL-12a , and interferon-d2.13. Combined, our results suggest that TLR25 is likely to play an important role in the antimicrobial responses of the innate immune system of Nile tilapia. • OnTLR25 is expressed at higher levels in immune-related organs. • OnTLR25 expression levels were significantly elevated by LPS, LTA, and zymosan. • Bacterial infection induced OnTLR25 transcription. • OnTLR25 preferentially localizes to the intracellular compartment. • Overexpression of truncated OnTLR25 activates immune-related signaling pathways. [ABSTRACT FROM AUTHOR]

Human‐generated noises are considered as underwater sound pollution with potential short‐ or long‐term impacts on behavioural responses and physiological reaction of aquatic living organisms. Few investigations are available so far on long‐term influences of impulsive and continuous sound sources on physiological response of fish. In the present study, opercula beat rates and pectoral wing rates were monitored as a physiological stress response of ventilation in Nile tilapia (Oreochromis niloticus) exposed to long‐term repeated and continued sounds generated from underwater construction work. Fish responded to underwater sound treatment with significantly increased opercula beat—and pectoral wing movements. Maximum ventilation rate was observed as a startle response of fish at initial exposure to underwater sound. The ventilation rates remained at high levels over the first 4 weeks and showed a declining trend thereafter. Fish growth was almost stable for the first 4 weeks, but shifted forward from day 45 onwards. We found strong evidence that fish could attune to repeated playbacks of underwater noise exposures since we found higher specific growth rates for the sound exposed fish from day 45 onwards until day 120, a so‐called 'catch‐up growth endeavour'. [ABSTRACT FROM AUTHOR]

Many species change their coloration during ontogeny or even as adults. Color change hereby often serves as sexual or status signal. The cellular and subcellular changes that drive color change and how they are orchestrated have been barely understood, but a deeper knowledge of the underlying processes is important to our understanding of how such plastic changes develop and evolve. Here we studied the color change of the Malawi golden cichlid (Melanchromis auratus). Females and subordinate males of this species are yellow and white with two prominent black stripes (yellow morph; female and non-breeding male coloration), while dominant males change their color and completely invert this pattern with the yellow and white regions becoming black, and the black stripes becoming white to iridescent blue (dark morph; male breeding coloration). A comparison of the two morphs reveals that substantial changes across multiple levels of biological organization underlie this polyphenism. These include changes in pigment cell (chromatophore) number, intracellular dispersal of pigments, and tilting of reflective platelets (iridosomes) within iridophores. At the transcriptional level, we find differences in pigmentation gene expression between these two color morphs but, surprisingly, 80% of the genes overexpressed in the dark morph relate to neuronal processes including synapse formation. Nerve fiber staining confirms that scales of the dark morph are indeed innervated by 1.3 to 2 times more axonal fibers. Our results might suggest an instructive role of nervous innervation orchestrating the complex cellular and ultrastructural changes that drive the morphological color change of this cichlid species. [ABSTRACT FROM AUTHOR]

Salinity represents a critical environmental factor for fishes, and it can directly influence their survival. Transcriptomic analysis at the gene expression level has been extensively conducted to identify functional genes or pathways involved in salinity adaptation in numerous euryhaline fishes. However, the post-transcriptional regulation mechanism in response to salinity changes remains largely unknown. Alternative splicing (AS), the main mechanism accounting for the complexity of the transcriptome and proteome in eukaryotes, plays essential roles in determining organismal responses to environmental changes. In this study, RNA-Seq datasets were used to examine the AS profiles in spotted sea bass (Lateolabrax maculatus), a typical euryhaline fish species. The results showed that 8618 AS events were identified in spotted sea bass. Furthermore, a total of 501 and 162 differential alternative splicing (DAS) events were characterized in the gill and liver under low- and high-salinity environments, respectively. Based on GO enrichment results, DAS genes in both the gill and liver were commonly enriched in 8 GO terms, and their biological functions were implicated in many stages of gene expression regulation, including transcriptional regulation and post-transcriptional regulation. Sanger sequencing and qPCR validations provided additional evidence to ensure the accuracy and reliability of our bioinformatic results. This is the first comprehensive view of AS in response to salinity changes in fish species, providing insights into the post-regulatory molecular mechanisms of euryhaline fishes in salinity adaptation. • A total of 8618 AS events were identified in spotted sea bass. • High-salinity environment significantly induced the generation of AS events in both gill and liver. • DAS genes in gill and liver were commonly enriched in various stages of gene expression regulation. [ABSTRACT FROM AUTHOR]

Infectious diseases represent a major threat for the sustainable development of fish farming. Efficient vaccines are not available against all diseases, and growing antibiotics resistance limits the use of antimicrobial drugs in aquaculture. It is therefore important to understand the basis of fish natural resistance to infections to help genetic selection and to develop new approaches against infectious diseases. However, the identification of the main mechanisms determining the resistance or susceptibility of a host to a pathogenic microbe is challenging, integrating the complexity of the variation of host genetics, the variability of pathogens, and their capacity of fast evolution and adaptation. Multiple approaches have been used for this purpose: (i) genetic approaches, QTL (quantitative trait loci) mapping or GWAS (genome-wide association study) analysis, to dissect the genetic architecture of disease resistance, and (ii) transcriptomics and functional assays to link the genetic constitution of a fish to the molecular mechanisms involved in its interactions with pathogens. To date, many studies in a wide range of fish species have investigated the genetic determinism of resistance to many diseases using QTL mapping or GWAS analyses. A few of these studies pointed mainly toward adaptive mechanisms of resistance/susceptibility to infections; others pointed toward innate or intrinsic mechanisms. However, in the majority of studies, underlying mechanisms remain unknown. By comparing gene expression profiles between resistant and susceptible genetic backgrounds, transcriptomics studies have contributed to build a framework of gene pathways determining fish responsiveness to a number of pathogens. Adding functional assays to expression and genetic approaches has led to a better understanding of resistance mechanisms in some cases. The development of knock-out approaches will complement these analyses and help to validate putative candidate genes critical for resistance to infections. In this review, we highlight fish isogenic lines as a unique biological material to unravel the complexity of host response to different pathogens. In the future, combining multiple approaches will lead to a better understanding of the dynamics of interaction between the pathogen and the host immune response, and contribute to the identification of potential targets of selection for improved resistance. [ABSTRACT FROM AUTHOR]

Anthropogenic underwater noise may negatively affect marine animals. Yet, while fishes are highly sensitive to sounds, effects of acoustic disturbances on fishes have not been extensively studied at the population level. In this study, we use a size-structured model based on energy budgets to analyse potential population-level effects of anthropogenic noise on Atlantic cod (Gadus morhua). Using the model framework, we assess the impact of four possible effect pathways of disturbance on the cod population growth rate. Through increased stress, changes in foraging and movement behaviour, and effects on the auditory system, anthropogenic noise can lead to (i) increased energy expenditure, (ii) reduced food intake, (iii) increased mortality, and (iv) reduced reproductive output. Our results show that population growth rates are particularly sensitive to changes in energy expenditure and food intake because they indirectly affect the age of maturation, survival and fecundity. Sub-lethal effects of sound exposure may thus affect populations of cod and fishes with similar life histories more than lethal effects of sound exposure. Moreover, anthropogenic noise may negatively affect populations when causing persistent increases of energy expenditure or decreases of food intake. Effects of specific acoustic pollutants on energy acquisition and expenditure should therefore be further investigated. [ABSTRACT FROM AUTHOR]

Pannexin 1 (Panx1) forms ATP-permeable membrane channels that play roles in the nervous system. The analysis of roles in both standard and pathological conditions benefits from a model organism with rapid development and early onset of behaviors. Such a model was developed by ablating the zebrafish panx1a gene using TALEN technology. Here, RNA-seq analysis of 6 days post fertilization larvae were confirmed by Real-Time PCR and paired with testing visual-motor behavior and in vivo electrophysiology. Results demonstrated that loss of panx1a specifically affected the expression of gene classes representing the development of the visual system and visual processing. Abnormal swimming behavior in the dark and the expression regulation of pre-and postsynaptic biomarkers suggested changes in dopaminergic signaling. Indeed, altered visuomotor behavior in the absence of functional Panx1a was evoked through D1/D2-like receptor agonist treatment and rescued with the D2-like receptor antagonist Haloperidol. Local field potentials recorded from superficial areas of the optic tectum receiving input from the retina confirmed abnormal responses to visual stimuli, which resembled treatments with a dopamine receptor agonist or pharmacological blocking of Panx1a. We conclude that Panx1a functions are relevant at a time point when neuronal networks supporting visual-motor functions undergo modifications preparing for complex behaviors of freely swimming fish. [ABSTRACT FROM AUTHOR]

Differences in social status are often mediated by agonistic encounters between competitors. Robust literature has examined social status-dependent brain gene expression profiles across vertebrates, yet social status and reproductive state are often confounded. It has therefore been challenging to identify the neuromolecular mechanisms underlying social status independent of reproductive state. Weakly electric fish, Gymnotus omarorum, display territorial aggression and social dominance independent of reproductive state. We use wild-derived G. omarorum males to conduct a transcriptomic analysis of non-breeding social dominance relationships. After allowing paired rivals to establish a dominance hierarchy, we profiled the transcriptomes of brain sections containing the preoptic area (region involved in regulating aggressive behaviour) in dominant and subordinate individuals. We identified 16 differentially expressed genes (FDR < 0.05) and numerous genes that co-varied with behavioural traits. We also compared our results with previous reports of differential gene expression in other teleost species. Overall, our study establishes G. omarorum as a powerful model system for understanding the neuromolecular bases of social status independent of reproductive state. [ABSTRACT FROM AUTHOR]

Anthropogenic activities are causing increased noise levels in the marine environment. To date, few studies have been undertaken to investigate the effects of different noise frequencies on the behaviour of juvenile fish. In this study, the behavioural changes of juvenile gilthead seabream (Sparus aurata) are evaluated when exposed to white noise filtered in third-octave bands centred at 63, 125, 500, and 1000 Hz (sound pressure level, 140–150 dB re 1 μΡa) for 7 h. The group dispersion, motility, and swimming height of the fish were analysed before and during the acoustic emission. Dispersion of the fish was found to reduce immediately upon application of low frequency sound (63 and 125 Hz) with a return to control condition after 2 h (indicative of habituation), whereas at 1 kHz, dispersion increased after 2 h without any habituation. The motility decreased significantly at 63 Hz throughout the 7 h of sound exposure. The swimming height decreased significantly for all frequencies other than 125 Hz. The results of this study highlight significant variations in the behavioural responses of juvenile fish that could have consequences on their fitness and survival. [ABSTRACT FROM AUTHOR]

Due to the absence of Automatic Identification System data (used by 3.7% of the Calvi bay fleet), the acoustic monitoring of coastal environments presents difficulties. A specific visual monitoring protocol has been set up on a photographic observatory using the wide-angle camera GoPro®. The detection and localization of boats were carried by two image processing algorithms and allowed the creation of a map of maritime traffic for a surface of 3.48 km2. The ocean noise is described through two different scales (the individual scale and the global scale) which are linked to the traffic information. The Sound Pressure Level characterizes the individual sources and correlates with the distance of the nearest ship, whereas the Ambient Noise Level characterizes the background without individual sources and correlates with the number of boats present. A high spatial and seasonal variability due to coastal maritime traffic is observed in the broadband [100 Hz–30 kHz]. Closest to the traffic, the acoustic is punctuated by diel patterns of biological sounds and the use patterns of the boaters. In spite of an important diurnal flotilla (more than 550 boats per day), the nocturnal activity of fish remains an important element on the soundscape (average and median levels higher during the night). [ABSTRACT FROM AUTHOR]

A six-week feeding trial was carried out to evaluate the effects of inclusion of dietary olive waste cake (OWC, 0, 0.5, 2.5 and 5 g kg−1 diet) on performance, antioxidant condition and immune responses of rainbow trout (Oncorhynchus mykiss) (2.5 ± 0.1 g). Supplementing diet with 2.5 and 5 g OWC kg−1 diet significantly enhanced serum and mucosal lysozyme activity in fish. Regarding mucosal immunity, fish fed 2.5 and 5 g OWC kg−1 diets had higher skin mucus total Ig concentrations than other groups. In relation to antioxidant status, those in 2.5 g OWC kg−1 and the control groups exhibited the highest and the least liver superoxide dismutase and glutathione peroxidase activities, respectively. Furthermore, the activity of liver glutathione S transferase in fish fed 2.5 and 5 g OWC kg−1 diets was higher than the other treatments. In respect to gut cytokines gene expression, our findings demonstrated dietary OWC did not influence interlukines-1β and 10 genes expression, but relative expression of IL8 gene gradually up-regulated with increasing dietary OWC level. Moreover, fish fed 0.5 g OWC kg−1 and the control diets had the highest and the lowest gut tumor necrosis factor-α gene expression values, respectively. The relative expression of transforming growth factor-β significantly down-regulated in gut of fish fed 2.5 and 5 g OWC kg−1 diets compared to other groups. Supplementing diet with OWC pronouncedly improved growth and feed conversion ratio in fish compared to the control. Overall, the findings of this study suggested that inclusion of 2.5 g OWC kg−1 diet can improve growth rate, oxidative stress status, humoral and skin mucosal immune responses in O. mykiss fingerlings and it can be considered as a functional feed additive for this species. • Dietary olive waste cake (OWC) increased serum immune parameters in trout fingerlings. • Trout fingerlings fed OWC showed altered mucosal immunity. • Feeding on OWC significantly increased the antioxidant enzymes activity. • Immune related genes were modulated by supplementing OWC in diet. [ABSTRACT FROM AUTHOR]

Fish are the most diverse vertebrate group, and they have evolved equally diverse visual systems, varying in terms of eye morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and opsin gene expression levels.This variation is mainly due to adaptations driven by two factors: differences in the light environments and behavioural tasks. However, while the effects of large‐scale habitat differences are well described, it is less clear whether visual systems also adapt to differences in environmental light at the microhabitat level.To address this, we assessed the relationship between microhabitat use and visual system features in fishes inhabiting coral reefs, where habitat partitioning is particularly common.We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology.We found that cardinalfishes display six types of microhabitat partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix.Species predominantly found in exposed microhabitats had higher expression of the short‐wavelength‐sensitive violet opsin (SWS2B) and lower expression of the dim‐light active rod opsin (RH1). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue‐green central part of the light spectrum (SWS2As and RH2s), while fishes entirely hidden in the reef substrate had a higher expression of the long‐wavelength‐sensitive red opsin.We also found that eye size relative to body size differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure.Retinal topography did not show co‐adaptation with microhabitat use, but data suggested co‐adaptation with feeding mode.We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems—and possibly those of other (reef) fishes—have also adapted to the light intensity and the light spectrum of their preferred diurnal microhabitats. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]