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Peroxisome proliferator–activated receptor γ (Pparγ) is a master regulator of adipogenesis. Chronic pathologies such as obesity, cardiovascular diseases, and diabetes involve the dysfunction of this transcription factor. Here, we generated a zebrafish mutant in pparγ (KO) with CRISPR/Cas9 technology and revealed its regulatory network. We uncovered the hepatic phenotypes of these male and female KO, and then the male wild-type zebrafish (WT) and KO were fed with a high-fat (HF) or standard diet (SD). We next conducted an integrated analyze of the proteomics and phosphoproteomics profiles. Compared with WT, the KO showed remarkable hyalinization and congestion lesions in the liver of males. Strikingly, pparγ deletion protected against the influence of high-fat diet feeding on lipid deposition in zebrafish. Some protein kinases critical for lipid metabolism, including serine/threonine-protein kinase TOR (mTOR), ribosomal protein S6 kinase (Rps6kb1b), and mitogen-activated protein kinase 14A (Mapk14a), were identified to be highly phosphorylated in KO based on differential proteome and phosphoproteome analysis. Our study supplies a pparγ deletion animal model and provides a comprehensive description of pparγ-induced expression level alterations of proteins and their phosphorylation, which are vital to understand the defective lipid metabolism risks posed to human health. [ABSTRACT FROM AUTHOR]

The stomach, which is characterized by acid peptic digestion in vertebrates, has been lost secondarily multiple times in the evolution of the teleost fishes. The Cypriniformes are largely seen as an agastric order; however, within the superfamily Cobitoidea, the closely related sister groups Nemacheilidae and Balitoridae have been identified as gastric families. The presence of these most recently diverged gastric families in an otherwise agastric clade indicates that either multiple (>2–3) loss events occurred with the Cyprinidae, Catostomidae and Cobitidae, or that gastric reinvention arose in a recent ancestor of the Nemacheilidae/Balitoridae sister clade. In the present study, the foregut regions of Cobitidae, Nemacheilidae/Balitoridae and the ancestral Botiidae family members were examined for the presence of gastric glands and gastric proton pump (Atp4a) α subunit expression by histology and immunohistochemistry respectively. Atp4a gene expression was assessed by reverse transcriptase-polymerase chain reaction (RT-PCR). Gastric glands expressing apical H+/K+-ATPase α subunit and isolated partial sequences of atp4a, identified using degenerate primers showing clear orthology to other vertebrate atp4a sequences, were detected in representative species from Nemacheilidae/ Balitoridae and Botiidae, but not Cobitidae (Misgurnus anguillicaudatus). In summary, we provide evidence for an uninterrupted gastric evolutionary lineage in the Cobitoidea, making it highly improbable that the stomach was reinvented in the Nemacheilidae/Balitoridae clade consistent with Dollo’s principle. These results also indicate that the gastric trait may be present elsewhere in the Cobitoidea. [ABSTRACT FROM AUTHOR]

Long-chain polyunsaturated fatty acids (LC-PUFA) are major components of complex lipid molecules and are also involved in numerous critical biological processes. Studies conducted mainly in vertebrates have demonstrated that LC-PUFA can be biosynthesized through the concerted action of two sets of enzymes, namely fatty acyl desaturases (Fads) and elongation of very long-chain fatty acid (Elovl) proteins. While LC-PUFA research is a thriving field, mainly focused on human health, an integrated view regarding the evolution of LC-PUFA biosynthetic genetic machinery in chordates is yet to be produced. Particularly important is to understand whether lineage specific life history trajectories, as well as major biological transitions, or particular genomic processes such as genome duplications have impacted the evolution of LC-PUFA biosynthetic pathways. Here we review the gene repertoire of Fads and Elovl in chordate genomes and the diversity of substrate specificities acquired during evolution. We take advantage of the magnitude of genomic and functional data to show that combination duplication processes and functional plasticity have generated a wide diversity of physiological capacities in extant lineages. A clear evolutionary framework is provided, which will be instrumental for the full clarification of functional capacities between the various vertebrate groups. [ABSTRACT FROM AUTHOR]

Both field and experimental data examined the influence of exposure to environmental contaminant tributyltin (TBT) on marine organisms. Although most attention focused on the imposex phenomenon in gastropods, adverse effects were also observed in other taxonomic groups. It has been shown that imposex induction involves modulation of retinoid signaling in gastropods. Whether TBT influences similar pathways in fish is yet to be addressed. In this study, larvae of the model teleostDanio reriowere exposed to natural retinoids, all-trans-retinoic acid, 9-cis-retinoic acid, and all-trans-retinol, as well as to the RXR synthetic pan-agonist methoprene acid (MA) and to TBT. Larvae were exposed to TBT from 5 days post fertilization (dpf) to adulthood, and reproductive capacity was assessed and correlated with mode of action. TBT significantly decreased fecundity at environmentally relevant levels at 1 μg TBT Sn/g in diet. Interestingly, in contrast to previous reports, TBT altered zebrafish sex ratio toward females, whereas MA exposure biased sex toward males. Since fecundity was significantly altered in the TBT-exposed group with up to 62% decrease, the potentially affected pathways were investigated. Significant downregulation was observed in brain mRNA levels of aromatase b (CYP19a1b) in females and peroxisome proliferator activated receptor gamma (PPARg) in both males and females, suggesting an involvement of these pathways in reproductive impairment associated with TBT. [ABSTRACT FROM PUBLISHER]

The stomach, a hallmark of gnathostome evolution, represents a unique anatomical innovation characterized by the presence of acid- and pepsinsecreting glands. However, the occurrence of these glands in gnathostome species is not universal; in the nineteenth century the French zoologist Cuvier first noted that some teleosts lacked a stomach. Strikingly, Holocephali (chimaeras), dipnoids (lungfish) and monotremes (egg-laying mammals) also lack acid secretion and a gastric cellular phenotype. Here, we test the hypothesis that loss of the gastric phenotype is correlated with the loss of key gastric genes.We investigated species from all the main gnathostome lineages and show the specific contribution of gene loss to the widespread distribution of the agastric condition.We establish that the stomach loss correlates with the persistent and complete absence of the gastric function gene kit�H�/K�- ATPase (Atp4A and Atp4B) and pepsinogens (Pga, Pgc, Cym)�in the analysed species. We also find that in gastric species the pepsinogen gene complement varies significantly (e.g. two to four in teleosts and tens in some mammals) with multiple events of pseudogenization identified in various lineages. We propose that relaxation of purifying selection in pepsinogen genes and possibly proton pump genes in response to dietary changes led to the numerous independent events of stomach loss in gnathostome history. Significantly, the absence of the gastric genes predicts that reinvention of the stomach in agastric lineages would be highly improbable, in line with Dollo�s principle. [ABSTRACT FROM AUTHOR]

Highlights: [•] Until recently, the presence of an elaborated retinoid system was believed to be a chordate/vertebrate novelty. [•] Patella depressa has the capacity to store retinoids in the form of inactive retinyl esters. [•] The imposex-susceptible species Nucella lapillus and Nassarius reticulatus lacked detectable amounts of retinol or retinyl esters. [•] An exposure test with N. lapillus confirmed that this species is not able to synthesize retinyl esters in vivo. [•] The incapacity to inactivate retinoid precursors might negatively affect retinoid signaling homeostasis. [ABSTRACT FROM AUTHOR]

Abstract: A negative correlation between female gonadal maturation kinetics and size variations of hepatic peroxisomes was earlier documented in brown trout, as a probable impact of serum estrogen changes during the reproductive cycle. Herein, we investigated whether the organelle volume/surface dynamics seen in female brown trout liver peroxisomes – without numerical changes within each hepatocyte – is followed by variations in the expression of the membrane peroxisome protein Pex11α gene. For comparison, we also studied males. We find in females a seasonal variation with the highest Pex11α expression in February, which was statistically different from all other tested periods. Overall, the expression of PEX11α had over a fivefold decrease from February to September. This period coincides with the reproductive transition between the earlier post-spawning gonadal remodeling and preparatory staging and the pre-spawning period. Males did not show changes. Our approach allowed the first characterization of a peroxin gene in a teleost, the Pex11α, while offering a correlation scenario were, as we hypothesized, the peroxisomal size kinetics is paralleled by membrane-related gene alterations (measured herein as proxy of Pex11α gene expression). Our data support and expand previous results on the regulation, function and morphology of peroxisome dynamics in brown trout, with a broader interest. [Copyright &y& Elsevier]

Abstract: Acetyl-CoA short chain synthetases (ACSSs) are key enzymes in the activation of fatty acids through the formation of thioesters with CoA. Three subfamily members are currently recognized in the human genome, ACSS1, ACSS2 and ACSS3, all single copy genes. The mitochondrial isoform, Acss1, plays a key role in the metabolism of acetate for energy production. While the single copy condition has been accurately established in humans, the evolutionary history of the Acss1 subfamily in vertebrates has yet to be elucidated, in particular, the isoform diversity, origin and function. Through genome database mining we analyzed the diversity of Acss1 isoforms in vertebrate classes. We detected the presence of a novel Acss1 isoform, which we name Acss1B. This new gene, Acss1B, has a curious phylogenetic distribution being found in teleosts (except zebrafish), sauropsids (birds and reptiles) and probably chondrichthyes. In contrast Acss1A is found in all the investigated species, except the teleost medaka. By means of comparative genomics and phylogenetics we show that Acss1A and Acss1B were generated in the quadruplication of the vertebrate genome. In effect, we find that amphioxus, a pre-genome duplication chordate, has a single Acss1 gene in a genomic region equally related to a quadrupled vertebrate genomic set. Consequently, Acss1B has been lost in some teleosts, amphibians and mammals, while Acss1A is probably absent in medaka. The reported findings illustrate an especially dynamic pattern of paralogue retention and independent loss in vertebrate species involving the Acss1 subfamily, whose functional consequences in energy metabolism are as yet unknown. [Copyright &y& Elsevier]

Although retinoids have been reported to be present and active in vertebrates and invertebrates, the presence of mechanisms for retinoid storage in the form of retinyl esters, a key feature to maintain whole-organism retinoid homeostasis, have been considered to date a vertebrate innovation. Here we demonstrate for the first time the presence of retinol and retinyl esters in an invertebrate lophotrochozoan species, the gastropod mollusk Osilinus lineatus. Furthermore, through a pharmacological approach consisting of intramuscular injections of different retinoid precursors, we also demonstrate that the retinol esterification pathway is active in vivo in this species. Interestingly, retinol and retinyl esters were only detected in males, suggesting a gender-specific role for these compounds in the testis. Females, although lacking detectable levels of retinol or retinyl esters, also have the biochemical capacity to esterify retinol, but at a lower rate than males. The occurrence of retinyl ester storage capacity, together with the presence in males and females of active retinoids, i.e., retinoic acid isomers, indicates that O. lineatus has a well developed retinoid system. Hence, the present data strongly suggest that the capacity to maintain retinoid homeostasis has arisen earlier in Bilateria evolution than previously thought. [ABSTRACT FROM AUTHOR]

Abstract: Retinoid X receptors (RXR) are transcription factors with important roles in development, reproduction, homeostasis, and cell differentiation. Different types of vertebrate RXRs (α (RXRA), ß (RXRB) and γ (RXRG)) have arisen from multiple duplication events. The adaptive evolution mechanism that has preserved duplicate RXR paralogs, as well as their role in development and adaptation, is thus far unknown. In this work, we have investigated different aspects of vertebrate RXR evolution. Codon based tests of positive selection identified that RXR was under significant positive selection immediately after the whole genome duplications in vertebrates. Amino acid based rate shift analysis also revealed significant rate shifts immediately after the whole genome duplications and functional divergence between all the pairs of RXRs. However, the extant RXR genes are highly conserved, particularly the helix involved in dimerization and the DNA-binding domain, but positively selected sites can nevertheless be found in domains for RXR regulation. [Copyright &y& Elsevier]

Abstract: Retinoids (vitamin A) are known to be involved in many key biological functions in mammals, such as embryonic development, reproduction or vision. Besides standard vitamin A forms, freshwater fish tissues contain high levels of didehydroretinoids or vitamin A2 forms. However, the tissue distribution, metabolism and function of both standard and particularly the didehydroretinoids are still poorly known in fish. In this study, we have quantified the levels of retinoids, including retinol, retinaldehyde, retinyl palmitate and their corresponding didehydro forms, as well as the levels of the active polar retinoids all-trans-, 9-cis- and 13-cis-retinoic acid in distinct tissues of juvenile rainbow trout. Our results indicate that the liver is clearly the main retinoid storage tissue in juvenile rainbow trout. Didehydroretinoids were dominant over retinoids in all analyzed tissues with the exception of plasma. Additionally, significant differences among tissues were observed between retinoids and didehydroretinoids, such as differences in the ester profiles and the proportions between free and esterified forms, suggesting that mechanisms that favor the utilization or storage of one of the other groups of compounds might exist in fish. Our data also show the presence of polar retinoids in different tissues of fish at the fmol/g scale. Overall, this study clearly demonstrates the presence of tissue-specific patterns of accumulation of both polar and nonpolar retinoids in fish tissues. The biological relevance of these findings should be the focus of future studies. [Copyright &y& Elsevier]

Background: Stearoyl-CoA desaturases (SCDs) are key enzymes involved in de novo monounsaturated fatty acid synthesis. They catalyze the desaturation of saturated fatty acyl-CoA substrates at the delta-9 position, generating essential components of phospholipids, triglycerides, cholesterol esters and wax esters. Despite being crucial for interpreting SCDs roles across species, the evolutionary history of the SCD gene family in vertebrates has yet to be elucidated, in particular their isoform diversity, origin and function. This work aims to contribute to this fundamental effort. Results: We show here, through comparative genomics and phylogenetics that the SCD gene family underwent an unexpectedly complex history of duplication and loss events. Paralogy analysis hints that SCD1 and SCD5 genes emerged as part of the whole genome duplications (2R) that occurred at the stem of the vertebrate lineage. The SCD1 gene family expanded in rodents with the parallel loss of SCD5 in the Muridae family. The SCD1 gene expansion is also observed in the Lagomorpha although without the SCD5 loss. In the amphibian Xenopus tropicalis we find a single SCD1 gene but not SCD5, though this could be due to genome incompleteness. In the analysed teleost species no SCD5 is found, while the surrounding SCD5-less locus is conserved in comparison to tetrapods. In addition, the teleost SCD1 gene repertoire expanded to two copies as a result of the teleost specific genome duplication (3R). Finally, we describe clear orthologues of SCD1 and SCD5 in the chondrichthian, Scyliorhinus canicula, a representative of the oldest extant jawed vertebrate clade. Expression analysis in S. canicula shows that whilst SCD1 is ubiquitous, SCD5 is mainly expressed in the brain, a pattern which might indicate an evolutionary conserved function. Conclusion: We conclude that the SCD1 and SCD5 genes emerged as part of the 2R genome duplications. We propose that the evolutionary conserved gene expression between distinct lineages underpins the importance of SCD activity in the brain (and probably the pancreas), in a yet to be defined role. We argue that an expression independent of an external stimulus, such as diet induced activity, emerged as a novel function in vertebrate ancestry allocated to the SCD5 isoform in various tissues (e.g. brain and pancreas), and it was selectively maintained throughout vertebrate evolution. [ABSTRACT FROM AUTHOR]

Abstract: Previously, it was documented that liver peroxisomes display seasonal size changes in the adult Salmo trutta fario, especially in females (and negatively correlated with ovary maturation). It was then hypothesized that decreases in peroxisome size could be paralleled by changes in peroxisomal β-oxidation and estradiol catabolism actions. The 17β-hydroxysteroid dehydrogenase 4 has been portrayed as playing an important role in both processes. To elucidate its function in the described peroxisomal pattern, we isolated the cDNA and predicted the protein sequence of the enzyme in that species. The seasonal gene expression pattern in both genders was addressed through quantitative PCR. Fish sampling was in post-spawning period, early and advanced gonad maturation, and pre-spawning. Males did not vary seasonally. As to females, a seasonal pattern was evidenced according to our previous hypothesis. We suggest that the decreased levels observed during vitellogenesis are related to lipid needs for ovary maturation, and, additionally, with the need of modulating estradiol titers. [Copyright &y& Elsevier]

Abstract: The imposex phenomenon in female prosobranch gastropods provides one of the best documented examples of endocrine disruption in wildlife. While many field studies have demonstrated the negative impact of tributyltin (TBT) upon female gastropods, the mechanism(s) underlying imposex development has not yet been fully clarified. Over the years several hypotheses have been raised to determine the biochemical and molecular determinants of this process. Nevertheless, the interplay between the different suggested pathways (neuroendocrine, steroid and retinoid) is still unknown. Hence, through a combination of exposure experiments, we show that the 9-cis-retinoic acid (9cisRA), the proposed natural ligand of the retinoic X receptor (RXR), induces imposex in females of Nucella lapillus to the same degree as tributyltin, when administered at similar concentrations (1μg/g body weight). Methoprene acid, a selective ligand for RXR, also induces imposex, albeit to a lower degree than that of the positive control. In contrast, testosterone significantly induced imposex, but had no effect on female penis induction, while the neuropeptide APGWamide had no effect on imposex development. These results clearly demonstrate that imposex induction in N. lapillus is mediated through the modulation of the RXR signalling pathways. In addition to the effects reported in female dogwhelks, both TBT and RA significantly increased male penis length, thus suggesting that TBT may also impact male secondary sex organs through the RXR signalling pathways. As a step for future studies, we have cloned the orthologue of N. lapillus RXR and provide experimental evidence that it binds 9cisRA. Finally, the basal expression level of RXR in several tissues of N. lapillus was determined through real-time PCR, thus showing that RXR is ubiquitously expressed in mollusc tissues, with the highest expression levels being recorded in female and male gonads. The mechanistic impacts of the overall findings to the imposex process are discussed. [Copyright &y& Elsevier]

Abstract: The molecular targets of estrogenic endocrine disrupting chemicals have been studied in detail in vertebrates. The lack of basic endocrine knowledge impairs similar approaches for invertebrates. Evidence indicates that the signalling pathways of invertebrates may also be a target of estrogenic chemicals (ECs). In fact, the exposure to effluents containing ECs has been reported to impact mollusc reproduction. Despite the reported estrogen independence of the mollusc nuclear estrogen receptor (ER), its role in EC-induced toxicity has not been investigated in vivo. Therefore, we have cloned the ER of the gastropod Nucella lapillus and evaluated the effects of a mixture of estrogenic chemicals (sewage effluent) on its expression in the ovary. Here, we show that the exposure to a raw domestic/industrial effluent, impact ER expression with a simultaneous reproductive maturation. These results highlight the need to further investigate the role of ER on the reproductive process in prosobranch gastropods and whether this signalling pathway is prone to disruption by ECs. [Copyright &y& Elsevier]

Abstract: In the vertebrate central nervous system (CNS), mutual antagonism between posteriorly expressed Gbx2 and anteriorly expressed Otx2 positions the midbrain/hindbrain boundary (MHB), but does not induce MHB organizer genes such as En, Pax2/5/8 and Wnt1. In the CNS of the cephalochordate amphioxus, Otx is also expressed anteriorly, but En, Pax2/5/8 and Wnt1 are not expressed near the caudal limit of Otx, raising questions about the existence of an MHB organizer in amphioxus. To investigate the evolutionary origins of the MHB, we cloned the single amphioxus Gbx gene. Fluorescence in situ hybridization showed that, as in vertebrates, amphioxus Gbx and the Hox cluster are on the same chromosome. From analysis of linked genes, we argue that during evolution a single ancestral Gbx gene duplicated fourfold in vertebrates, with subsequent loss of two duplicates. Amphioxus Gbx is expressed in all germ layers in the posterior 75% of the embryo, and in the CNS, the Gbx and Otx domains abut at the boundary between the cerebral vesicle (forebrain/midbrain) and the hindbrain. Thus, the genetic machinery to position the MHB was present in the protochordate ancestors of the vertebrates, but is insufficient for induction of organizer genes. Comparison with hemichordates suggests that anterior Otx and posterior Gbx domains were probably overlapping in the ancestral deuterostome and came to abut at the MHB early in the chordate lineage before MHB organizer properties evolved. [Copyright &y& Elsevier]

Abstract: In an attempt to clarify the mechanism(s) of tributyltin-mediated imposex induction in females of the neogastropod Nucella lapillus, dogwhelks collected in an almost imposex free population were exposed to several treatments for a 3 month-period, and the effects on imposex induction and testosterone/estradiol levels were evaluated. As a positive control, tributyltin (50 ng TBT Sn/L) clearly induced imposex and led to a significant increase in the severity of the phenomenon. In contrast, although a selective P450 aromatase inhibitor (formestane at 0.3 mg/L) was capable of imposex induction, it failed to increase its severity. A vertebrate androgen receptor (AR) antagonist (cyproterone acetate at 1.25 mg/L) in combination with TBT completely blocked the imposex induction capacity of TBT. On the other hand, an estrogen receptor antagonist (tamoxifen at 0.3 mg/L) rendered no effect. The determination of steroid levels in female specimens revealed that TBT induces an elevation of free testosterone (but not the total amount, free+esterified), while the co-administration of the anti-androgen and TBT was able to rescue the increase of free testosterone levels. Despite a minor decrease in the amount of testosterone–fatty acid esters in the TBT group, significant differences in esterified testosterone were not found among treatments. On the contrary, free estradiol levels were elevated in the TBT, anti-androgens and TBT plus anti-androgens groups. These results indicate that free estradiol biosynthesis in TBT-exposed females does not seem to be affected. Overall, our results demonstrate that a selective aromatase inhibitor can induce imposex in N. lapillus but not to a similar extent of TBT, which may suggest the involvement of other mechanism in imposex induction, besides aromatase inhibition. Additionally, the study points to the involvement of AR receptors in imposex induction. [Copyright &y& Elsevier]

The Drosophila melanogaster genome has six physically clustered NK-related homeobox genes in just 180 kb. Here we show that the NK homeobox gene cluster was an ancient feature of bilaterian animal genomes, but has been secondarily split in chordate ancestry. The NK homeobox gene clusters of amphioxus and vertebrates are each split and dispersed at two equivalent intergenic positions. From the ancestral NK gene cluster, only the Tlx-Lbx and NK3-NK4 linkages have been retained in chordates. This evolutionary pattern is in marked contrast to the Hox and ParaHox gene clusters, which are compact in amphioxus and vertebrates, but have been disrupted in Drosophila. [ABSTRACT FROM AUTHOR]

Background: Habitat transitions have considerable consequences in organism homeostasis, as they require the adjustment of several concurrent physiological compartments to maintain stability and adapt to a changing environment. Within the range of molecules with a crucial role in the regulation of different physiological processes, neuropeptides are key agents. Here, we examined the coding status of several neuropeptides and their receptors with pleiotropic activity in Cetacea. Results: Analysis of 202 mammalian genomes, including 41 species of Cetacea, exposed an intricate mutational landscape compatible with gene sequence modification and loss. Specifically for Cetacea, in the 12 genes analysed we have determined patterns of loss ranging from species-specific disruptive mutations (e.g. neuropeptide FF-amide peptide precursor; NPFF) to complete erosion of the gene across the cetacean stem lineage (e.g. somatostatin receptor 4; SSTR4). Conclusions: Impairment of some of these neuromodulators may have contributed to the unique energetic metabolism, circadian rhythmicity and diving response displayed by this group of iconic mammals. [ABSTRACT FROM AUTHOR]

The article focuses on nuclear receptor (NR)-mediated endocrine disruption in invertebrates. It states that NR is part of a superfamily of ligand-dependent and independent transcription factors responsible for regulating many biological processes including metabolism, morphogenesis, and differentiation. It suggests that the phylogenetic distribution and molecular specificity of NR binding profile is linked to the animal taxonomic scope of NR-mediated endocrine disruptions.

The MHC genes on human chromosome 6 are located within one of the best-characterised paralogy regions of the human genome. Numerous genes mapping around this location, 6p21, have paralogues at one, two or three other chromosomal locations on HSA 1, 9 and 19. The similarity between these four chromosomal regions suggests the linkages may have adaptive significance, and/or they may be echoes of segmental or genome duplication in human ancestry. Here, we show that six amphioxus cosmids, containing genes orthologous to those from the human MHC-linked paralogy regions, map to a single amphioxus chromosome. The composition of the MHC-linked genomic region, therefore, pre-dates vertebrate origins. [ABSTRACT FROM AUTHOR]

Obesity is a rapidly growing health pandemic, underlying a wide variety of disease conditions leading to increases in global mortality. It is known that the phosphorylation of various proteins regulates sterol regulatory element-binding transcription factors 1 (srebf1), a key lipogenic transcription factor, to cause the development of obesity. To detect the key protein kinases for regulating srebf1 in lipid deposition, we established the srebf1 knockout model in zebrafish (KO, srebf1−/−) by CRISPR/Cas9. The KO zebrafish exhibited a significant reduction of total free fatty acid content (fell 60.5%) and lipid deposition decrease compared with wild-type (WT) zebrafish. Meanwhile, srebf1 deletion in zebrafish eliminated lipid deposition induced by high-fat diet feeding. Compared with WT zebrafish, a total of 697 differentially expressed proteins and 316 differentially expressed phosphoproteins with 439 sites were identified in KO by differential proteomic and phosphoproteomic analyses. A significant number of proteins identified were involved in lipid and glucose metabolism. Moreover, some protein kinases critical for regulating srebf1 in lipid deposition, including Cdk2, Pkc, Prkceb, mTORC1, Mapk12, and Wnk1, were determined by network analyses. An in vitro study was performed to verify the network analysis results. Our findings provide potential targets (kinases) for human obesity treatments. [ABSTRACT FROM AUTHOR]

Background: The S100A7 gene, also called psoriasin, was first described as an upregulated protein in psoriatic skin. For the past years, the importance of this protein as a key effector of innate immunity has been clearly established, not only due to its importance protecting against bacteria skin insult in humans, but also because of its important role in amplifying inflammatory processes. Given the importance of S100A7 in host defense, S100A7 genes have been mostly studied in humans. Here we provide a detailed analysis of the evolution of the gene family encoding for the S100A7 protein in mammals. Results: Examination of several mammalian genomes revealed an unexpected variation in the copy number of S100A7. Among the most representative mammalian groups, we report that multiple events of duplication, gene loss and high mutation rates are shaping the evolution of this gene family. An unexpected result comes from Myotis species (order Chiroptera), where we found an outstanding S100A7 gene radiation, resulting in more than 10 copies in M. lucifugus and 5 copies in M. brandtii. These findings suggest a unique adaptive road in these species and are suggestive of special role of this protein in their immune system. Conclusions: We found different evolutionary histories among different mammalian groups. Overall, our results suggest that this gene family is evolving under the birth-and-death model of evolution. To our knowledge, this work represents the first detailed analysis of phylogenetic relationships of S100A7 within mammals and therefore will pave the way to further clarify their unique function in the immune system. [ABSTRACT FROM AUTHOR]

Paracentrotus lividus is the most abundant echinoid species in the North East Atlantic Ocean and Mediterranean Sea. Although there is abundant genomic information of the species, there is no deep characterisation of the genes involved in the immune response. Here, a reference transcriptome of male and female coelomocytes was produced. The generated P. lividus transcriptome assembly has 203,511 transcripts, N50 transcript length of 1079 bp, and more than 90% estimated gene completeness in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses showed 54 and 55 up-regulated genes in P. lividus female and male coelomocyte tissues, respectively. These results suggest a similar immune gene repertoire between sexes. To examine the immune response, P. lividus was challenged with Vibrio anguillarum , one of the candidate pathogens for bald disease. Immune parameters were evaluated at cell and humoral levels, as well as the expression analysis of immune related genes at an early response stage. No differences were found at cellular and humoral levels with the exception of the increase of nitric oxide in perivisceral fluid of challenged animals. At the gene expression level, a total of 2721 genes were upregulated in challenged animals, 13.6 times higher expression than control group. Our analysis revealed that four major KEGG pathways were enriched in challenged animals: Autophagy (KEGG:04140), Endocytosis (KEGG:04144), Phagosome (KEGG:04145) and Protein processing in endoplasmic reticulum (KEGG:04141). Several toll-like receptors (TLR), scavenger receptors cysteine-rich (SRCR) or nucleotide-binding oligomerisation domain like receptors (NLR) were identified as major family genes for pathogen recognition and immune defence. This study provides a valuable transcriptomic resource and unfolds the molecular basis of immune response to V. anguillarum exposure. Overall, our findings contribute to the conservation effort of the P. lividus populations, as well as its sustainable exploitation in an aquaculture context. • A reference transcriptome of Paracentrotus lividus coelomocytes was built. • Regarding gene expression between sexes no significant differences were founded. • Challenge against Vibrio anguillarum reveal a high upregulation of genes at 4 h post exposure. • Four major KEGG pathways were significantly enriched: autophagy, endocytosis, phagosome and PPER. • No differences were founded at short term in humoral or cellular responses. [ABSTRACT FROM AUTHOR]

Mollusca is the second most species-rich phylum within the metazoans, displaying critical economic, ecological and scientific importance. Yet, they are still largely underrepresented with respect to genomic resources. The emergence of next-generation sequencing technologies has revolutionized deep-scale genomic characterization of non-model organisms, and molluscs are slowly entering this transformative era. Here, we provide a historical contextualization of the Genome Revolution in molluscs with a tour de force revision of key research trends observed over the past decade. Omic approaches such as RAD-seq, transcriptome, mitogenome and whole-genome sequencing represent the most significant resources produced for this phylum. Importantly, the molecular mechanisms underscoring multiple biological novelties and adaptations observed in molluscs are starting to be unravelled. In contrast, compared to other metazoan lineages the genomic resources currently available for this lineage still lag far behind. We put forward that to fully grasp the evolutionary and adaptive roads of this tantalizing group of organisms crucially depends on the full embracement of high-throughput sequencing (HTS) technologies in the near future. [ABSTRACT FROM AUTHOR]

The striped eel catfish, Plotosus lineatus was first described by Thunberg in 1787 from the Indo-Pacific region in the East Indian Ocean. Since then, the species has been recorded in various marine and brackish habitats in Japan, southern Korea, the Ogasawara Islands, Australia, Lord Howe Island, Palau and Yap in Micronesia, East Africa to Samoa, Madagascar, Red Sea and the Persian Gulf. Occurrences of this species have also been registered in the Mediterranean Sea, a non-native location, indicating a possible biological invasion event. Despite its long history, the taxonomic status of the P. lineatus species complex remains puzzling and uncertain. Here, we analysed all the available mitochondrial cytochrome c oxidase subunit 1 sequences (NCBI and BOLD) from specimens covering the current known distribution range, in an attempt to clarify the evolutionary relationships of different lineages within this species. We deduce nine monophyletic Lineages - I–IX, of P. lineatus with Kimura-2P distances ranging from 2% to 16%, with a mean intraspecific distance of 6%. Strikingly, Lineage V is composed uniquely of Mediterranean-captured individuals, with an unknown evolutionary origin. These findings strongly suggest the need for a careful species taxonomic reassessment. Some Lineages are composed of individuals from specific geographic locations (e.g., Australia and Indonesia), while others include specimens from broader geographic areas (e.g., almost all Indo-Pacific coastline). Additionally, several deposited sequences are most likely the result of morphology-based misidentifications. Due to the biological invasive potential, as well as the use of the species as a valuable physiology model, the P. lineatus species complex requires further attention. Overall our study offers a clear framework for future comparative studies of striped eel catfish individuals captured from different ecosystems. [ABSTRACT FROM AUTHOR]

Thyroid hormones (THs) are the only iodine-containing hormones that play fundamental roles in chordates and non-chordates. The chemical nature, mode of action and the synthesis of THs are well established in mammals and other vertebrates. Although thyroid-like hormones have been detected in protostomes and non-chordate deuterostomes, TH signaling is poorly understood as compared to vertebrates, particularly in protostomes. Therefore, the central objective of this article is to review TH system components and TH-induced effects in non-vertebrate chordates, non-chordate deuterostomes and protostomes based on available genomes and functional information. To accomplish this task, we integrate here the available knowledge on the THs signaling across non-vertebrate chordates, non-chordate deuterostomes and protostomes by considering studies encompassing TH system components and physiological actions of THs. We also address the possible interactions of thyroid disrupting chemicals and their effects in protostomes and non-chordate deuterostomes. Finally, the perspectives on current and future challenges are discussed. Unlabelled Image • The biological significance of THs in non-vertebrate deuterostomes and protostomes is reviewed. • THs have the ability to induce pleotropic effects across invertebrates. • TH system is a target of endocrine disrupting chemicals. [ABSTRACT FROM AUTHOR]

The common bottlenose dolphin (Tursiops truncatus) is a top marine predator widely dispersed in coastal and pelagic habitats and with a generalist feeding behavior. Yet, information on the trophic ecology of animals inhabiting pelagic environments is still scarce. Using carbon (δ13C: 13C/12C) and nitrogen (δ15N: 15N/14N) stable isotope ratios, we identified and quantified the main groups of prey assimilated by bottlenose dolphins inhabiting an oceanic habitat (Madeira Island, East Atlantic). Bottlenose dolphins assimilated pelagic, schooling fish (such as blue jack mackerel, Trachurus picturatus) and mesopelagic and demersal squids, which reinforces the pelagic dietary composition of insular/oceanic dolphins. Also, intra-seasonal differences were found in their stable isotope ratios, which suggest intraspecific variability in the feeding behavior among individuals living in the same area. Sex was not the main factor contributing to these differences, suggesting the lack of trophic niche segregation between adult males and females in this offshore environment. Nonetheless, further studies including different life stages and information on the ecophysiological requirements are necessary to disclose the factors responsible for the observed variability. This study showed that insular dolphins fed primarily on economically important pelagic prey, highlighting the need of developing management strategies that integrate conservation in fisheries plans. [ABSTRACT FROM AUTHOR]

The mammalian skin exhibits a rich spectrum of evolutionary adaptations. The pilosebaceous unit, composed of the hair shaft, follicle, and the sebaceous gland, is the most striking synapomorphy. The evolutionary diversification of mammals across different ecological niches was paralleled by the appearance of an ample variety of skin modifications. Pangolins, order Pholidota, exhibit keratin-derived scales, one of the most iconic skin appendages. This formidable armor is intended to serve as a deterrent against predators. Surprisingly, while pangolins have hair on their abdomens, the occurrence of sebaceous and sweat glands is contentious. Here, we explore various molecular modules of skin physiology in four pangolin genomes, including that of sebum production. We show that genes driving wax monoester formation, Awat1/2, show patterns of inactivation in the stem pangolin branch, while the triacylglycerol synthesis gene Dgat2l6 seems independently eroded in the African and Asian clades. In contrast, Elovl3 implicated in the formation of specific neutral lipids required for skin barrier function is intact and expressed in the pangolin skin. An extended comparative analysis shows that genes involved in skin pathogen defense and structural integrity of keratinocyte layers also show inactivating mutations: associated with both ancestral and independent pseudogenization events. Finally, we deduce that the suggested absence of sweat glands is not paralleled by the inactivation of the ATP-binding cassette transporter Abcc11, as previously described in Cetacea. Our findings reveal the sophisticated and complex history of gene retention and loss as key mechanisms in the evolution of the highly modified mammalian skin phenotypes. [ABSTRACT FROM AUTHOR]

The highly diverse group of freshwater mussels from order Unionida is found in the world's freshwater systems due to several fascinating evolutionary adaptations, including "parental care," and most notably, an obligatory parasitic phase in their early life cycle, called glochidia, which infests and uses fish for nutrition and dispersal. Freshwater mussels play essential ecological roles in freshwater habitats, including water filtration, sediment bioturbation, and nutrient cycling. However, these species are also highly threatened, being one of the faunal groups with the highest recorded extinction rate in the wild. Genomics methods have an incredible potential to promote biodiversity conservation, allowing the characterization of population health, identification of adaptive genetic elements, delineation of conservation units, and providing a framework for predictive assessments of the impact of anthropogenic threats and climate change. Unfortunately, only six freshwater mussel species have had their whole genomes sequenced to date, and only two of these are European species. Here, we present the first genome assembly of the Painter's Mussel, Unio pictorum (Linnaeus, 1758), the type species representative of the order and the most widespread species of the genus in Europe. We used long-read PacBio Hi-Fi sequencing reads to produce a highly contiguous assembly that will pave the way for the study of European freshwater mussels in the Genome Era. [ABSTRACT FROM AUTHOR]

The eccentric seahorses, seadragons, pipehorses and pipefishes (Syngnathidae) have an aglomerular kidney 1. Here, we show that nephron genes 2 conserved in Bilateria are secondarily eroded/deleted in Syngnathidae genomes. A transcriptome enrichment analysis suggests the predominance of excretion processes in the Syngnathidae kidney. In a lineage where crypsis and idleness are tightly associated, we propose that aglomerulism evolved as an energy-saving strategy. The family of fishes that includes seahorses, seadragons, pipehorses and pipefishes has unusual kidneys that lack glomeruli. Pinto et al. show that this is accompanied by the loss of glomerulus-related genes, including several required for re-absorption of nutrients and other metabolites, which they speculate may be an energy-saving adaptation. [ABSTRACT FROM AUTHOR]

Background: Over the past decade, variations of the coding portion of the human genome have become increasingly evident. In this study, we focus on polymorphic pseudogenes, a unique and relatively unexplored type of pseudogene whose inactivating mutations have not yet been fixed in the human genome at the global population level. Thus, polymorphic pseudogenes are characterized by the presence in the population of both coding alleles and non-coding alleles originating from Loss-of-Function (LoF) mutations. These alleles can be found both in heterozygosity and in homozygosity in different human populations and thus represent pseudogenes that have not yet been fixed in the population. Results: A methodical cross-population analysis of 232 polymorphic pseudogenes, including 35 new examples, reveals that human olfactory signalling, drug metabolism and immunity are among the systems most impacted by the variable presence of LoF variants at high frequencies. Within this dataset, a total of 179 genes presented polymorphic LoF variants in all analysed populations. Transcriptome and proteome analysis confirmed that although these genes may harbour LoF alleles, when the coding allele is present, the gene remains active and can play a functional role in various metabolic pathways, including drug/xenobiotic metabolism and immunity. The observation that many polymorphic pseudogenes are members of multigene families argues that genetic redundancy may play a key role in compensating for the inactivation of one paralogue. Conclusions: The distribution, expression and integration of cellular/biological networks in relation to human polymorphic pseudogenes, provide novel insights into the architecture of the human genome and the dynamics of gene gain and loss with likely functional impact. [ABSTRACT FROM AUTHOR]

Aquaculture of carnivorous fish species heavily relies on marine ingredients to guarantee the provision of essential nutrients, including long-chain (C 20 – 24) polyunsaturated fatty acids (LC-PUFA) such as arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3), and docosahexaenoic acid (DHA, 22:6n-3). These nutrients are crucial for fish growth and neural development, offering significant health benefits to consumers. The rapid growth of global aquaculture production in recent decades, has driven the exploration of alternative and sustainable feeding sources that ensure n-3 LC-PUFA content. Within the context of circular economy, polychaete worms arise as promising candidates for aquafeed formulations, due to the enzymatic capacity for de novo LC-PUFA biosynthesis. The present study focused on the molecular and functional characterisation of elongases (Elovl) and front-end desaturases (Fed) involved in the LC-PUFA biosynthesis of the nereid polychaete Hediste diversicolor. The sequence and phylogenetic analysis established the orthology of three Elovl, identified as Elovl2/5, Elovl4 and Elovl1/7, that have putative functions in the LC-PUFA biosynthesis. Functional characterisation in yeast demonstrated their roles as PUFA elongases, exhibiting affinity towards C 18 and C 20 PUFA substrates (Elovl2/5) and towards C 18 , C 20 and C 22 (Elovl4 and Elovl1/7). Additionally, H. diversicolor possesses two front-end desaturases (Fed1 and Fed2) with Δ5 and Δ6/Δ8 desaturation activities, respectively, thus encompassing all the necessary desaturation reactions involved in the LC-PUFA biosynthesis pathways. These findings, along with the previously characterised methyl-end desaturases, show that H. diversicolor possesses the full enzymatic repertoire necessary to produce LC-PUFA like ARA and EPA. This highlights the potential of polychaetes and other annelids for producing nutrient-rich biomass suitable for aquaculture. • H. diversicolor has three elongases with affinity for C18–22 PUFA substrates. • H. diversicolor has two desaturases with Δ5 and Δ6/Δ8 activities. • H. diversicolor has all necessary machinery for biosynthesis of EPA and ARA. • Current evidence does not support DHA synthesis in H. diversicolor. [ABSTRACT FROM AUTHOR]

Abstract: In fish, some ABC transporters are implicated in a multixenobiotic resistance (MXR) mechanism to deal with the presence of xenobiotics, by effluxing them, or their metabolites, from inside the cells. These efflux transporters have been considered an integral part of cellular detoxification pathways, acting in coordination with phase I and II detoxification enzymes. However, the full characterization of this detoxification system is still incomplete, especially during the developmental stages of aquatic organisms, which are particularly sensitive periods to the presence of anthropogenic contamination. The goal of this study was to evaluate the mRNA expression dynamics of putatively important MXR proteins (ABCB1b, ABCB11, ABCC1, ABCC2 and ABCG2a) and phase I (CYP1A) and II (GSTα) biotransformation enzymes, during the embryonic and larval developments of the specie Oreochromis niloticus (Nile tilapia). Our results showed that ABCB1b, ABCC1, CYP1A and GSTα transcripts are maternally transmitted. Transcripts for ABCB11, ABCC2 and ABCG2a were only detected after the pharyngula period, which precedes a highly sensitive stage in the embryonic development, the hatching. This study has shown, for the first time, very distinct expression patterns of genes encoding for proteins involved in protection mechanisms against pollutants during the development of Nile tilapia. Moreover, the temporal pattern of gene expression suggests that increased intrinsic protection levels are required at specific developmental stages. [Copyright &y& Elsevier]

Abstract: The aim of this study was to evaluate the response of ABC transporters, CYP1A and class alpha (α) GST genes, upon water and dietary exposures to benzo(a)pyrene (BaP) in Oreochromis niloticus. Partial mRNA sequences of ABC transporters (ABCB1b, ABCB11, ABCC1, ABCC2 and ABCG2) were identified, and their tissue distribution patterns evaluated in liver, gill and intestine, showing similarities with other fish and mammals. After 14days of water exposure to BaP, ABC transporters mRNA expression was up-regulated, namely ABCC2 in gill (up to 16-fold) and ABCG2 in liver (up to 2-fold) and proximal intestine (up to 7-fold). CYP1A mRNA expression was up-regulated in water exposed animals, with maximum fold inductions of 5, 35 and 155, respectively in liver, gill and proximal intestine. After dietary exposure, intestinal CYP1A mRNA showed a 13-fold increase in exposed animals. No significant changes were seen in ABCB1b, ABCC1 and GSTα mRNA expression after both routes of exposure to BaP. In conclusion, this study has shown that transcriptional expression of some ABC transporters and CYP1A respond to the presence of BaP, indicating a possible involvement and cooperation in the detoxification process in Nile tilapia. [Copyright &y& Elsevier]

Many environmental pollutants can exert adverse effects on exposed organisms, including fish, leading to disruption of the endocrine system. Enzymes involved in the sex steroid biosynthesis are potential targets for the toxic action of pollutants. In this context, we investigated the hypothesis that selected estrogenic chemicals-the pharmaceutical estrogen ethinylestradiol (EE2), the phytoestrogen genistein (GEN), and the industrial compound bisphenol A (BPA)-may cause endocrine disruption by directly disturbing steps of fish steroidogenic pathways. We studied the mRNA expression of eight selected genes encoding steroidogenic enzymes (11β-HSD2, 20β-HSD, 3β-HSD1, 17β-HSD1, 17β-HSD8, 17β-HSD12, CYP19a, CYP19b) by quantitative real-time PCR. Testis slices from adult specimens of the model fish Nile tilapia were exposed in vitro for 3 and 8 h either to individual or to mixture solutions of EE2 (100 ng/L), GEN (200 ng/L), and BPA (10 µg/L); all at the peak concentrations observed in the Douro River estuary (Portugal). Our data revealed that only the mixture of the tested chemicals directly induced the expression of 11β-HSD2, 17β-HSD1, and 17β-HSD12, after 8 h, whereas no effect was seen for chemicals tested individually. The gene expression pattern agrees with the concept of dose addition for environmental mixtures, and for the first time an interference of estrogenic EDCs is reported for 17β-HSD1 and 17β-HSD12. [ABSTRACT FROM AUTHOR]

Abstract: PPAR isotypes have been previously identified in the teleost brown trout (Salmo trutta f. fario) and their organ distribution pattern established. Being that the liver is a vital metabolic organ presenting expression of all isotypes and also knowing that estrogens/estrogen receptors seem to interact with PPARs, we hypothesized that the latter may very well change seasonally. So, we studied the expression of these receptors in the liver, along the annual reproductive cycle and in both genders. According to real-time RT-PCR, PPARα mRNA expression in females was significantly higher in May and lower in September than in other seasons. No significant variation was observed along the year in males. A significant difference between genders occurred in May, when PPARα expression was higher for females. PPARβ expression showed little variation along the reproductive cycle in females, but in males it was significantly higher in December than in the other seasons. No significant differences existed between genders. PPARγ was more expressed in February than in September and December, for females. As to males, it was more expressed in February than in all other seasons. No significant differences were observed between genders. The study proved our hypothesis that PPARs gene expression varies along the year. Moreover, PPARα expression in females followed the same annual variation pattern as peroxisome volumes and enzyme activities, and an inverse pattern relatively to the salmonid type annual plasma estradiol levels. The data agrees with the idea that PPARα is under estradiol modulation and that cross-talk between this receptor and the estrogen receptor possibly exists. [Copyright &y& Elsevier]

Abstract: The presence of estrogenic chemicals (ECs) in the aquatic environment is a growing problem. While most attention was initially given to fresh water and estuarine ecosystems, it is now evident that coastal marine areas are also vulnerable to these pollutants. The use of vitellogenin induction in male fish, a specific biomarker of EC exposure, has been the most widely applied methodology. However, in some occasions, the high mobility and migratory behaviour of common sentinel fish species makes data interpretation difficult. Hence, there is the need to validate new sentinel marine fish species which should display, among other features, a strong homing behaviour. The shanny, Lipophrys pholis, is an intertidal fish that combines many of the required characteristics for a sentinel species: abundance and easy of catch, wide geographical distribution and restricted home range. Thus, in order to evaluate, in the field, the species sensitivity to ECs, L. pholis males were collected at two sites reflecting different degrees of anthropogenic contamination. The vitellogenin II gene (VTGII) was isolated and its liver expression evaluated by RT-PCR in the field samples. A significant induction of gene expression was observed in the specimens collected in the urban area, if compared to the reference site, which suggests exposure to ECs. Moreover, a 21-days laboratory exposure to environmental relevant concentrations of ethinylestradiol (EE2) was also performed. A significant induction of L. pholis VTGII gene in EE2 exposed males was observed suggesting similar sensitivity to that of other marine/estuarine fishes. Even though further validation is currently in progress, the available data indicates that L. pholis is responsive to ECs, thus favouring its future integration in monitoring programmes designed to evaluate the presence of ECs in European marine ecosystems. [Copyright &y& Elsevier]

Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters, and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e., Linnaeus's two-toed sloth), but undetected in other closely related species (i.e., brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were probably lost independently among Xenarthra orders. Additionally, by expanding our analysis to 157 mammal genomes, we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia, and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy and endorses the use of genomic analyses to ascertain the physiological status of suspected vestigial structures. [ABSTRACT FROM AUTHOR]

Given the ecological unsustainability of using fish oil (FO) as the main source of long‐chain polyunsaturated fatty acids (LC‐PUFA), the investigation of alternative dietary LC‐PUFA sources is crucial for aquaculture. Tambaqui (Colossomamacropomum) is a valuable economic aquaculture resource in Brazil, capable of endogenously elongating and desaturating linoleic (LA; 18:2n‐6) and α‐linolenic (ALA; 18:3n‐3) acids to longer and physiologically vital LC‐PUFA. Yet, it is unclear how this pathway is regulated by different oil sources in tambaqui. Thus, we designed an experiment with 2 different oil diets (fish oil—FO and vegetable oil—VO) at 2 different concentrations (5% or 10%) to investigate the molecular regulation of fatty acid biosynthesis in this species. We observed no differences in survival, body weight gain (BWG) and feed conversion ratio between the treatments. Gene expression analysis shows that fads2andelovl5 are up‐regulated in liver, while fads2 and elovl2 are up‐regulated in brain of tambaqui fed with VO. The transcription factors pparβbandpparγ are also up‐regulated in the brain by VO diet, when compared to FO diet. The VO diet also contributed to the biosynthesis of LC‐PUFA in liver and specifically DHA in the brain. Overall, our approach shows that lipid metabolism‐relevant genes are regulated by different dietary lipid sources. [ABSTRACT FROM AUTHOR]

The ancestors of Cetacea underwent profound morpho-physiological alterations. By displaying an exclusive aquatic existence, cetaceans evolved unique patterns of locomotor activity, vigilant behaviour, thermoregulation and circadian rhythmicity. Deciphering the molecular landscape governing many of these adaptations is key to understand the evolution of phenotypes. Here, we investigate Cortistatin (CORT), a neuropeptide displaying an important role in mammalian biorhythm regulation. This neuropeptide is a known neuroendocrine factor, stimulating slow-wave sleep, but also involved in the regulation of energy metabolism and hypomotility inducement. We assessed the functional status of CORT in 359 mammalian genomes (25 orders), including 30 species of Cetacea. Our findings indicate that cetaceans and other mammals with atypical biorhythms, thermal constraints and/or energy metabolism, have accumulated deleterious mutations in CORT. In light of the pleiotropic action of this neuropeptide, we suggest that this inactivation contributed to a plethora of phenotypic adjustments to accommodate adaptive solutions to specific ecological niches. • CORT was independently pseudogenized across several mammalian orders. • CORT loss parallels adaptive shifts in sleeping behaviour in cetaceans. • CORT loss possibly contributed to changes in energy homeostasis in carnivores. • CORT pseudogenization supports the role of gene loss in phenotypic adaptation. [ABSTRACT FROM AUTHOR]

• Classical class II genes were found in Cartilaginous fish genomes and transcriptomes. • Sharks show ancient lineages (>350 MY) of class II α and β genes. • α and β genes are arranged in lineage-specific pairs of linked genes. • Class II lineages clearly segregate as pseudoalleles in nurse sharks. • Nonclassical class II DM is absent from Cartilaginous fish and from basal vertebrates. Cartilaginous fish (chimaeras, rays and sharks) are the most basal extant jawed vertebrates with an adaptive immune system based on the Major Histocompatibility Complex (MHC). Despite being a key taxon in the evolution of vertebrate adaptive immunity, no comprehensive characterization of MHC class II genes has been undertaken for the group. We performed extensive bioinformatic searches on a taxonomically diverse dataset of transcriptomes and genomes of cartilaginous fish targeting MHC class II sequences. Class IIα and IIβ sequences were retrieved from all taxa analyzed and showed typical features of classical class II genes. Phylogenetic trees of the immunoglobulin superfamily domain showed two divergent and remarkably ancient lineages of class II genes in Selachians (sharks), originating >350 million years ago. Close linkage of lineage-specific pairs of IIα and IIβ genes was found, confirming previous results, with genes from distinct lineages segregating as alleles. Nonclassical class II DM sequences were not retrieved from these data and classical class II sequences lacked the conserved residues shown to interact with DM molecules, supporting claims that the DM system arose only in the lobe-finned fish lineage leading to tetrapods. Based on our search methods, other divergent class II genes are unlikely in cartilaginous fish. [ABSTRACT FROM AUTHOR]

Abstract The deep-sea is the biggest ecosystem in the world and is characterized by extreme conditions such as high pressure, low temperatures and absence or limited light. Despite the scarce studies due to inaccessibility, these ecosystems are considered highly biodiverse. The deep-sea is subjected to anthropogenic stressors with deep-sea mining being a likely new form of disruption. Understanding how it affects the surrounding environments is paramount to develop guidelines to protect sensitive habitats and allow for responsible exploitation of resources. One of the potential stressors associated with deep-sea mining are the sediment laden plumes that can be generated during the mining process. The present study examined, for the first time, the effects of suspended sediments (0, 1, 2 and 4 g/L) in the model mussel species, Mytilus galloprovincialis , under hyperbaric conditions (1, 4 and 50 Bar). Functional endpoints, i.e. feeding assays, together with biochemical biomarkers of oxidative stress [catalase (CAT), lipid peroxidation (LPO), glutathione-s-transferase (GST) and superoxide dismutase (SOD)] were studied in juvenile mussels. The filtration rate (FR) of M. galloprovincialis decreased with the increment in the sediment concentrations, for all tested pressure conditions (1, 4 and 50 Bar). Significant alterations were also observed for all tested biomarkers, being sediment and pressure-dependent. Interestingly, pressure had an effect in GST activity, that increased in the 4 and 50 Bar experiments in comparison with the results at 1 Bar. Remarkably, filtration rates were significantly affected by pressure. These findings will support the filling of the knowledge gaps related with the hazard assessment of deep-sea mining associated stressors. Graphical abstract Unlabelled Image Highlights • Study of deep-sea mining associated stressors in mussel digestive gland • Impact of suspended sediments in mussels under hyperbaric conditions • Hydrostatic pressure showed significant effect at functional and biochemical levels. • Suspended sediments caused disturbances in the functional and biochemical response. [ABSTRACT FROM AUTHOR]

The appearance of mammalian-specific skin features was a key evolutionary event contributing for the elaboration of physiological processes such as thermoregulation, adequate hydration, locomotion, and inflammation. Skin inflammatory and autoimmune processes engage a population of skin-infiltrating T cells expressing a specific C-C chemokine receptor (CCR10) which interacts with an epidermal CC chemokine, the skin-specific C-C motif chemokine ligand 27 (CCL27). CCL27 is selectively produced in the skin by keratinocytes, particularly upon inflammation, mediating the adhesion and homing of skin-infiltrating T cells. Here, we examined the evolution and coding condition of Ccl27 in 112 placental mammalian species. Our findings reveal that a number of open reading frame inactivation events such as insertions, deletions, and start and stop codon mutations independently occurred in Cetacea, Pholidota, Sirenia, Chiroptera, and Rodentia, totalizing 18 species. The diverse habitat settings and lifestyles of Ccl27-eroded lineages probably implied distinct evolutionary triggers rendering this gene unessential. For example, in Cetacea, the rapid renewal of skin layers minimizes the need for an elaborate inflammatory mechanism, mirrored by the absence of epidermal scabs. Our findings suggest that the convergent and independent loss of Ccl27 in mammalian evolution concurred with unique adaptive roads for skin physiology. [ABSTRACT FROM AUTHOR]

Abstract The crosstalk between peroxisome proliferator-activated receptor α (PPARα) and estrogenic pathways are shared from fish to humans. Salmonid fish had an additional genome duplication, and two PPARα isoforms (PPARαBa and PPARαBb) were previously identified. Since a negative regulation between estrogen signaling and PPARα was described, a post-transcriptional gene silencing for PPARαBb was designed in primary brown trout hepatocytes. The aims of the study were to: (i) decipher the effects of PPARαBb knock-down on peroxisome morphology and on mRNA expression of potential target genes, and (ii) to assess the cross-interferences caused by an estrogenic compound (17α-ethinylestradiol – EE2) and a PPARα agonist (Wy-14,643 – Wy) using the established knock-down model. A knock-down efficiency of 70% was achieved for PPARαBb and its silencing significantly reduced the volume density of peroxisomes, but did not alter mRNA levels of the studied genes. Exposure to Wy did not change peroxisome morphology or mRNA expression, but under silencing conditions Wy rescued the volume density of peroxisomes to control levels, and increased acyl-coenzyme A oxidase 1-3l (Acox1-3l) mRNA. Exposure to EE2 caused a reduction of peroxisome volume density, but under silencing conditions this effect was abolished and ApoA1 mRNA level was diminished. The morphological alterations of peroxisomes by WY and EE2 demonstrated that obtained results are PPARαBb dependent, and suggest the regulation of unknown downstream targets of PPARαBb. In summary, PPARαBb is involved in the control of peroxisome size and/or number, which opens future opportunities to explore its regulation and molecular targets. Graphical abstract Unlabelled Image Highlights • PPARαBb isoform was successfully silenced in primary brown trout hepatocytes. • PPARαBb gene silencing reduced significantly the volume density of peroxisomes. • No alterations of mRNA level on potential PPARα target genes were observed. • An estrogen and a PPARα agonist affected silencing and peroxisome morphology. • PPARαBb is involved in the control of peroxisome size and/or number. [ABSTRACT FROM AUTHOR]

Highlights • RAR unresponsiveness towards retinoic acid is conserved in molluscs from Bivalvia, Gastropoda and Polyplacophora classes. • Using an in vitro assay, N. lapillus RAR did not respond to pesticides Endrin and Dieldrin, unlike the human homologue. • In molluscs, the RAR/RXR heterodimer yields transcriptional repression upon exposure to retinoids or RXR-specific ligands. • The repressive behaviour is conserved in the human heterodimer upon exposure to RXR-specific ligands. Abstract Retinoid acid receptor (RAR)-dependent signalling pathways are essential for the regulation and maintenance of essential biological functions and are recognized targets of disruptive anthropogenic compounds. Recent studies put forward the inability of mollusc RARs to bind and respond to the canonical vertebrate ligand, retinoic acid: a feature that seems to have been lost during evolution. Yet, these studies were carried out in a limited number of molluscs. Therefore, using an in vitro transactivation assay, the present work aimed to characterize phylogenetically relevant mollusc RARs, as monomers or as functional units with RXR, not only in the presence of vertebrate bone fine ligands but also known endocrine disruptors, described to modulate retinoid-dependent pathways. In general, none of the tested mollusc RARs were able to activate reporter gene transcription when exposed to retinoic acid isomers, suggesting that the ability to respond to retinoic acid was lost across molluscs. Similarly, the analysed mollusc RAR were unresponsive towards organochloride pesticides. In contrast, transcriptional repressions were observed with the RAR/RXR unit upon exposure to retinoids or RXR-specific ligands. Loss-of-function and gain-of-function mutations further corroborate the obtained results and suggest that the repressive behaviour, observed with mollusc and human RAR/RXR heterodimers, is possibly mediated by ligand biding to RXR. [ABSTRACT FROM AUTHOR]

Abstract In vertebrates, the essential fatty acids (FA) that satisfy the dietary requirements for a given species depend upon its desaturation and elongation capabilities to convert the C 18 polyunsaturated fatty acids (PUFA), namely linoleic acid (LA, 18:2n-6) and α-linolenic acid (ALA, 18:3n–3), into the biologically active long-chain (C 20–24) polyunsaturated fatty acids (LC-PUFA), including arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3). Recent studies have established that tambaqui (Colossoma macropomum), an important aquaculture-produced species in Brazil, is a herbivorous fish that can fulfil its essential FA requirements with dietary provision C 18 PUFA LA and ALA, although the molecular mechanisms underpinning such ability remained unclear. The present study aimed at cloning and functionally characterizing genes encoding key desaturase and elongase enzymes, namely fads2 , elovl5 and elovl2 , involved in the LC-PUFA biosynthetic pathways in tambaqui. First, a fads2 -like desaturase was isolated from tambaqui. When expressed in yeast, the tambaqui Fads2 showed Δ6, Δ5 and Δ8 desaturase capacities within the same enzyme, enabling all desaturation reactions required for ARA, EPA and DHA biosynthesis. Moreover, tambaqui possesses two elongases that are bona fide orthologs of elovl5 and elovl2. Their functional characterization confirmed that they can operate towards a variety of PUFA substrates with chain lengths ranging from 18 to 22 carbons. Overall our results provide compelling evidence that demonstrates that all the desaturase and elongase activities required to convert LA and ALA into ARA, EPA and DHA are present in tambaqui within the three genes studied herein, i.e. fads2 , elovl5 and elovl2. Graphical abstract Unlabelled Image Highlights • Tambaqui Fads2 has Δ6, Δ5 and Δ8 desaturase capacities within the same enzyme. • Tambaqui possess both Elovl5 and Elovl2 enzymes enabling elongation of C 18–22 PUFA substrates. • Tambaqui has desaturase and elongase activities required to biosynthesize ARA, EPA and DHA from dietary C 18 precursors. [ABSTRACT FROM AUTHOR]

The Cetacea infraorder comprises a very unique group within the mammalian lineage. While sharing common ancestors with terrestrial mammals, their exclusive dependence on aquatic environments makes them attractive models to explore the landscape of molecular shifts in radical habitat transitions. Among their diverse anatomical and physiological solutions, we find detectable genetic remodeling of the immune system. In agreement, here we show that the gene sequence of interleukin-20 (IL20) displays unambiguous signs of inactivation with several disruptive mutations, including stop codons, insertions, and a conserved trans-species mutation abolishing a canonical splice site, in nine analyzed cetacean genomes. Considering the suggested role of IL20 in skin immunity processes, including inflammation, epithelization, and remodeling, we propose that gene inactivation follows specific adaptations of cetacean skin to the aquatic environment, in frame with the less-is-more hypothesis. [ABSTRACT FROM AUTHOR]

Lipid metabolism involves complex pathways, which are regulated in a similar way across vertebrates. Hormonal and hypolipidemic deregulations cause lipid imbalance from fish to humans, but the underlying mechanisms are far from understood. This study explores the potential of using juvenile brown trout to evaluate the in vivo interferences caused by estrogenic (17α-ethinylestradiol – EE2), androgenic (testosterone – T), and hypolipidemic (clofibrate – CLF) compounds in lipidic and/or peroxisomal pathways. Studied endpoints were from blood/plasma biochemistry, plasma fatty acid profile, ultrastructure of hepatocytes and abundance of their peroxisomes to mRNA expression in the liver. Both T and CLF caused minimal effects when compared to EE2. Estrogenized fish had significantly higher hepatosomatic indexes, increased triglycerides and very-low density lipoproteins (VLDL) in plasma, compared with solvent control. Morphologically, EE2 fish showed increased lipid droplets in hepatocytes, and EE2 and T reduced volume density of peroxisomes in relation to the hepatic parenchyma. Polyunsaturated fatty acids (PUFA) in plasma, namely n−3 PUFA, increased with EE2. EE2 animals had increased mRNA levels of vitellogenin A (VtgA), estrogen receptor alpha (ERα), peroxisome proliferator-activated receptor alpha (PPARα), PPARαBa and acyl-CoA long chain synthetase 1 (Acsl1), while ERβ-1, acyl-CoA oxidase 1–3I (Acox1–3I), Acox3, PPARγ, catalase (Cat), urate oxidase (Uox), fatty acid binding protein 1 (Fabp1) and apolipoprotein AI (ApoAI) were down-regulated. In summary, in vivo EE2 exposure altered lipid metabolism and peroxisome dynamics in brown trout, namely by changing the mRNA levels of several genes. Our model can be used to study possible organism-level impacts, viz. in gonadogenesis. [ABSTRACT FROM AUTHOR]

Fatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FAs they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FAs with >16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2 , are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fishes, coelacanths and cartilaginous fishes named ACSBG3 . Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways. [ABSTRACT FROM AUTHOR]