Liver Transcriptome Changes in Zebrafish during Acclimation to Transport-Associated Stress

Liver plays a key role during the stress acclimation, and liver transcriptome analysis of shipped zebrafish could reveal the molecular adjustments that occur in the organ. Transcriptional changes in liver were analyzed with a 44 K oligo array using total RNA from fish prior to transport and during a mock transport process--immediately after packing (0 h), at 48 and 72 h. Large numbers of genes related to a variety of biological processes and pathways were regulated, mainly during transport (at 48/72 h). Immediately after packing, transcripts of genes related to both gluconeogenesis and glycolysis were induced. During transport, induction of gluconeogenesis-linked genes and reduction of glycolysis-related genes may be supporting the increase in blood glucose levels. Inhibition of genes involved in fatty acid beta-oxidation may be pointing to the poor ability of fish to utilize energy from fatty acids, under transport conditions. Genes involved in some of the mechanisms that regulate body ammonia were also affected. Even though genes associated with certain transaminases were inhibited in liver, sustained glutamate deamination may have led to high ammonia accumulation in liver/body. Enhanced levels of gene transcripts in ubiquitination and MAPK signalling cascade and reduced levels of gene transcripts related to ROS generation via peroxisomal enzymes as well as xenobiotic metabolism may be signifying the importance of such cellular and tissue responses to maintain homeostasis. Furthermore, transcripts connected with stress and thyroid hormones were also regulated. Moreover, suppression of genes related to specific immune components may be denoting the deleterious impact of transport on fish health. Thus, this study has revealed the complex molecular adjustments that occur in zebrafish when they are transported

Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus

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Changes in intestinal microbiota, immune- and stress-related transcript levels in Senegalese sole (Solea senegalensis) fed plant ingredient diets intercropped with probiotics or immunostimulants

Author's accepted version (post-print).Available from 04/03/2018.Senegalese sole (Solea senegalensis) is a highly valued flatfish that grows well with diets containing plant ingredients but their effects on immune competence is still a matter of debate. The current study aimed to examine changes in innate immune parameters and gut microbiota in Senegalese sole fed with 35% or 72% of plant ingredients with or without probiotic or yeast supplementation. Overall, fish fed diets with 72% of plant ingredients showed lower transcript levels of key immune- and stress-related genes in distal intestine, rectum and head-kidney than the 35% diets. In particular, hsp90b mRNA levels in distal intestine were down-regulated by 70% and 60% with the use of high content of plant ingredients in the diet containing the multispecies probiotic and autolyzed yeast, respectively. Denaturing gradient gel electrophoresis showed lower similarity values for distal intestine than rectum. Also fish fed high content of plant ingredients displayed lower similarity values, pointing to a difference in the microbial populations between fish fed different plant ingredients content on the diet. Our data revealed that inclusion of plant ingredients was associated with differences in gene expression and a more diverse microbiota profile but without a significant effect on growth performance. Moreover, probiotic supplementation resulted in up-regulation of hsp90b, gpx, cat and apoa1 transcript levels in distal intestine concomitantly with a growth rate reduction compared to non-supplemented fish

Effects of functional ingredients on gut inflammation in Atlantic salmon (Salmo salar L)

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Towards population genomics in non-model species with large genomes : a case study of the marine zooplankton Calanus finmarchicus

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Genetics redraws pelagic biogeography of Calanus

Planktonic copepods of the genus Calanus play a central role in North Atlantic/Arctic marine food webs. Here, using molecular markers, we redrew the distributional ranges of Calanus species inhabiting the North Atlantic and Arctic Oceans and revealed much wider and more broadly overlapping distributions than previously described. The Arctic shelf species, C. glacialis, dominated the zooplankton assemblage of many Norwegian fjords, where only C. finmarchicus has been reported previously. In these fjords, high occurrences of the Arctic species C. hyperboreus were also found. Molecular markers revealed that the most common method of species identification, prosome length, cannot reliably discriminate the species in Norwegian fjords. Differences in degree of genetic differentiation among fjord populations of the two species suggested that C. glacialis is a more permanent resident of the fjords than C. finmarchicus. We found no evidence of hybridization between the species. Our results indicate a critical need for the wider use of molecular markers to reliably identify and discriminate these morphologically similar copepod species, which serve as important indicators of climate responses.publishedVersionPaid Open Acces

Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype

Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits

Expression profiles of representative genes in selected GO categories.

<p>(A) Carbohydrate metabolic process; (B) Lipid metabolic process; (C) Proteolysis; (D) Amino acid metabolic process; and (E) Oxidation-reduction process. Significantly regulated genes –in at least one of the time points [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - are displayed in the heat maps. Columns and rows in the heat map indicate time points and genes, respectively. Color scale represents fold changes of gene expression. Genes belonging to more than one GO category is shown only once under a particular GO term. *indicates significant differences (P<0.05) at a particular time point compared to the expression of the respective genes prior to transport (basal).</p

Validation of microarray results by quantitative real time PCR.

<p>Correlation plots indicating the relationship between qPCR results (fold change; Y- axis)) of six selected genes and the corresponding data from microarray analysis (X- axis). Fold changes of genes immediately after packing (0 h), and at 48 and 72 h during transport compared to the values prior to transport (basal) are displayed in the figure. Note that the fold changes for <i>scd</i> are 1/10^th of the actual changes.</p

Expression profiles of representative genes in selected GO categories.

<p>(A) Response to stress; (B) Response to chemical stimulus; and (C) Cellular homeostasis. Significantly regulated genes – in at least one of the time points [immediately after packing (0 h), and at 48 and 72 h during transport] compared to the values prior to transport (basal) - are displayed in the heat maps. Columns and rows in the heat map indicate time points and genes, respectively. Color scale represents fold changes of gene expression. Genes belonging to more than one GO category is shown only once under a particular GO term. *indicates significant differences (P<0.05) at a particular time point compared to the expression of the respective genes before transport (basal).</p