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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Mélanie Debiais-Thibaud; Cushla J. Metcalfe; Jacob Pollack; Isabelle Germon; +5 Authors

    Background: The Dlx gene family encodes transcription factors involved in the development of a wide variety of morphological innovations that first evolved at the origins of vertebrates or of the jawed vertebrates. This gene family expanded with the two rounds of genome duplications that occurred before jawed vertebrates diversified. It includes at least three bigene pairs sharing conserved regulatory sequences in tetrapods and teleost fish, but has been only partially characterized in chondrichthyans, the third major group of jawed vertebrates. Here we take advantage of developmental and molecular tools applied to the shark Scyliorhinus canicula to fill in the gap and provide an overview of the evolution of the Dlx family in the jawed vertebrates. These results are analyzed in the theoretical framework of the DDC (Duplication-Degeneration-Complementation) model.Results: The genomic organisation of the catshark Dlx genes is similar to that previously described for tetrapods. Conserved non-coding elements identified in bony fish were also identified in catshark Dlx clusters and showed regulatory activity in transgenic zebrafish. Gene expression patterns in the catshark showed that there are some expression sites with high conservation of the expressed paralog(s) and other expression sites with events of paralog sub-functionalization during jawed vertebrate diversification, resulting in a wide variety of evolutionary scenarios within this gene family.Conclusion: Dlx gene expression patterns in the catshark show that there has been little neo-functionalization in Dlx genes over gnathostome evolution. In most cases, one tandem duplication and two rounds of vertebrate genome duplication have led to at least six Dlx coding sequences with redundant expression patterns followed by some instances of paralog sub-functionalization. Regulatory constraints such as shared enhancers, and functional constraints including gene pleiotropy, may have contributed to the evolutionary inertia leading to high redundancy between gene expression patterns. International audience

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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    Authors: López-Barneo, J; Nurse, C A; Nilsson, G E; Buck, L T; +2 Authors

    Survival success under conditions of acute oxygen deprivation depends on efficiency of the central and peripheral chemoreception, optimization of oxygen extraction from the hypoxic environment and its delivery to the periphery, and adjustments of energy production and consumption. This article uses a comparative approach to assess the efficiency of adaptive strategies used by anoxia-tolerant and hypoxia-sensitive species to support survival during the first minutes to 1 h of oxygen deprivation. An aquatic environment is much more demanding in terms of diurnal and seasonal variations of the ambient oxygen availability from anoxia to hyperoxia than is an air environment. Therefore, fishes and aquatic turtles have developed a number of adaptive responses, which are lacking in most of the terrestrial mammals, to cope with these extreme conditions. These include efficient central and peripheral chemoreception, acute changes in respiratory rate and amplitude, and acute increase of the gas-exchange interface. A special set of adaptive mechanisms are engaged in reduction of the energy expenditure of the major oxygen-consuming organs: the brain and the heart. Both reduction of ATP consumption and a switch to alterative energy sources contribute to the maintenance of ATP and ion balance in hypoxia-tolerant animals. Hypoxia and hyperoxia are conditions favoring development of oxidative stress. Efficient protection from oxidation in anoxia-tolerant species includes reduction in the glutamate levels in the brain, stabilization of the mitochondrial function, and maintenance of nitric oxide production under conditions of oxygen deprivation. We give an overview of the current state of knowledge on some selected molecular and cellular acute adaptive mechanisms. These include the mechanisms of chemoreception in adult and neonatal mammals and in fishes, acute metabolic adaptive responses in the brain, and the role of nitrite in the preservation of heart function under hypoxic conditions.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Physiological and Bi...arrow_drop_down
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    Physiological and Biochemical Zoology
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    https://doi.org/10.5167/uzh-43...
    Other literature type . 2010
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Physiological and Bi...arrow_drop_down
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      Physiological and Biochemical Zoology
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      https://doi.org/10.5167/uzh-43...
      Other literature type . 2010
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    Authors: Thomas Desvignes; Peter Batzel; Jason Sydes; B. Frank Eames; +1 Authors

    AbstractMicroRNAs (miRNAs) can have tissue-specific expression and functions; they can originate from dedicated miRNA genes, from non-canonical miRNA genes, or from mirror-miRNA genes and can also experience post-transcriptional variations. It remains unclear, however, which mechanisms of miRNA production or modification are tissue-specific and the extent of their evolutionary conservation. To address these issues, we developed the software Prost! (PRocessing Of Short Transcripts), which, among other features, allows accurate quantification of mature miRNAs, takes into account post-transcriptional processing, such as nucleotide editing, and helps identify mirror-miRNAs. Here, we applied Prost! to annotate and analyze miRNAs in three-spined stickleback (Gasterosteus aculeatus), a model fish for evolutionary biology reported to have a miRNome larger than most teleost fish. Zebrafish (Danio rerio), a distantly related teleost with a well-known miRNome, served as comparator. Despite reports suggesting that stickleback had a large miRNome, results showed that stickleback has 277 evolutionary-conserved mir genes and 366 unique mature miRNAs (excluding mir430 gene replicates and the vaultRNA-derived mir733), similar to zebrafish. In addition, small RNA sequencing data from brain, heart, testis, and ovary in both stickleback and zebrafish identified suites of mature miRNAs that display organ-specific enrichment, which is, for many miRNAs, evolutionarily-conserved. These data also supported the hypothesis that evolutionarily-conserved, organ-specific mechanisms regulate miRNA post-transcriptional variations. In both stickleback and zebrafish, miR2188-5p was edited frequently with similar nucleotide editing patterns in the seed sequence in various tissues, and the editing rate was organ-specific with higher editing in the brain. In summary, Prost! is a critical new tool to identify and understand small RNAs and can help clarify a species’ miRNA biology, as shown here for an important fish model for the evolution of developmental mechanisms, and can provide insight into organ-specific expression and evolutionary-conserved miRNA post-transcriptional mechanisms.

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    Scientific Reports
    Article . 2019
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    Scientific Reports
    Article . Preprint . 2019 . Peer-reviewed
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      Scientific Reports
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      Scientific Reports
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    Authors: Striberny, Anja; Jørgensen, Even H.; Klopp, Christophe; Magnanou, Elodie;

    Background: The Arctic charr (Salvelinus alpinus) has a highly seasonal feeding cycle that comprises long periods of voluntary fasting and a short but intense feeding period during summer. Therefore, the charr represents an interesting species for studying appetite-regulating mechanisms in fish. Results: In this study, we compared the brain transcriptomes of fed and feed deprived charr over a 4 weeks trial during their summer feeding season. Despite prominent differences in body condition between fed and feed deprived charr at the end of the trial, feed deprivation affected the brain transcriptome only slightly. In contrast, the transcriptome differed markedly over time in both fed and feed deprived charr, indicating strong shifts in basic cell metabolic processes possibly due to season, growth, temperature, or combinations thereof. The GO enrichment analysis revealed that many biological processes appeared to change in the same direction in both fed and feed deprived fish. In the feed deprived charr processes linked to oxygen transport and apoptosis were down- and up-regulated, respectively. Known genes encoding for appetite regulators did not respond to feed deprivation. Gene expression of Deiodinase 2 (DIO2), an enzyme implicated in the regulation of seasonal processes in mammals, was lower in response to season and feed deprivation. We further found a higher expression of VGF (non-acronymic) in the feed deprived than in the fed fish. This gene encodes for a neuropeptide associated with the control of energy metabolism in mammals, and has not been studied in relation to regulation of appetite and energy homeostasis in fish. Conclusions: In the Arctic charr, external and endogenous seasonal factors for example the increase in temperature and their circannual growth cycle, respectively, evoke much stronger responses in the brain than 4 weeks feed deprivation. The absence of a central hunger response in feed deprived charr give support for a strong resilience to the lack of food in this high Arctic species. DIO2 and VGF may play a role in the regulation of energy homeostasis and need to be further studied in seasonal fish. Source at https://doi.org/10.1186/s12864-019-5874-z. © The Author(s). 2019

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    BMC Genomics
    Article . 2019
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    BMC Genomics
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    BMC Genomics
    Article . 2019 . Peer-reviewed
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      BMC Genomics
      Article . 2019
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      BMC Genomics
      Article . 2019 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: M F, McLoughlin; D A, Graham; A, Norris; D, Matthews; +5 Authors

    Pancreas disease (PD) of farmed Atlantic salmon Salmo salar L., which is caused by an alphavirus known as salmon pancreas disease virus (SPDV), can have serious economic consequences. An epidemiological survey carried out in Ireland in 2003 indicated that within individual farms there were significant differences in the susceptibility of different strains of farmed Atlantic salmon to infection with SPDV, as measured by levels of clinical disease and mortality. The aim of this preliminary study was to investigate this field observation by comparing lesion development, viraemia and serological responses of 3 commercial strains of Atlantic salmon (A, B and C) experimentally infected with SPDV. Highly significant differences in the severity of lesions in the pancreas at Day 21 post-infection (pi) were detected (p < 0.01), with Group B being more severely affected. There were also significant differences in the prevalence and severity of lesions in heart and skeletal muscle at Day 21 and 35 pi respectively, with Group B results again significantly higher than those from both Groups A and C (p < 0.05). There was no overlap between viraemia and the presence of specific SPDV antibody. Some fish in all groups had no viraemia, lesions or evidence of seroconversion. There were no significant differences seen between the challenged groups in relation to the percentage of viraemic fish at each time point. Viral loads were not determined. Differences between the number of antibody-positive fish in each challenge group were found at Days 28 and 35 pi (p < 0.1). Highly significant differences (p < 0.01) in the geometric mean titres of seropositive fish were detected at Day 28. These results, obtained using a challenge model, confirm that there are strain differences in the susceptibility to experimental SPDV infection in commercial farmed Atlantic salmon.

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    Diseases of Aquatic Organisms
    Article . 2006 . Peer-reviewed
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      Diseases of Aquatic Organisms
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  • Authors: Elodie Magnanou; Christophe Klopp; Céline Noirot; Laurence Besseau; +1 Authors

    The sea bass Dicentrarchus labrax is the center of interest of an increasing number of basic or applied research investigations, even though few genomic or transcriptomic data is available. Current public data only represent a very partial view of its transcriptome. To fill this need, we characterized brain and liver transcriptomes in a generalist manner that would benefit the entire scientific community. We also tackled some bioinformatics questions, related to the effect of RNA fragment size on the assembly quality. Using Illumina RNA-seq, we sequenced organ pools from both wild and farmed Atlantic and Mediterranean fishes. We built two distinct cDNA libraries per organ that only differed by the length of the selected mRNA fragments. Efficiency of assemblies performed on either or both fragments size differed depending on the organ, but remained very close reflecting the quality of the technical replication. We generated more than 19,538Mbp of data. Over 193million reads were assembled into 35,073 contigs (average length=2374bp; N50=3257). 59% contigs were annotated with SwissProt, which corresponded to 12,517 unique genes. We compared the Gene Ontology (GO) contig distribution between the sea bass and the tilapia. We also looked for brain and liver GO specific signatures as well as KEGG pathway coverage. 23,050 putative micro-satellites and 134,890 putative SNPs were identified. Our sampling strategy and assembly pipeline provided a reliable and broad reference transcriptome for the sea bass. It constitutes an indisputable quantitative and qualitative improvement of the public data, as it provides 5 times more base pairs with fewer and longer contigs. Both organs present unique signatures consistent with their specific physiological functions. The discrepancy in fragment size effect on assembly quality between organs lies in their difference in complexity and thus does not allow prescribing any general strategy. This information on two key organs will facilitate further functional approaches. International audience

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    Authors: Elizabeth A. Nyboer; Lauren J. Chapman;

    Fishes faced with novel thermal conditions often modify physiological functioning to compensate for elevated temperatures. This physiological plasticity (thermal acclimation) has been shown to improve metabolic performance and extend thermal limits in many species. Adjustments in cardiorespiratory function are often invoked as mechanisms underlying thermal plasticity because limitations in oxygen supply have been predicted to define thermal optima in fishes, however few studies have explicitly linked cardiorespiratory plasticity to metabolic compensation. Here we quantify thermal acclimation capacity in the commercially harvested Nile perch (Lates niloticus) of East Africa, and investigate mechanisms underlying observed changes. We reared juvenile Nile perch for 3 months under two temperature regimes, and then measured a series of metabolic traits (e.g., aerobic scope, AS) and critical thermal maximum (CTmax) upon acute exposure to a range of experimental temperatures. We also measured morphological traits of heart ventricles, gills, and brains to identify potential mechanisms for compensation. We found that long-term (3-months) exposure to elevated temperature induced compensation in upper thermal tolerance (CTmax) and metabolic performance (SMR, MMR and AS), and induced cardiac remodeling in Nile perch. Furthermore, variation in heart morphology influenced variations in metabolic function and thermal tolerance. These results indicate that plastic changes enacted over longer exposures lead to differences in metabolic flexibility when acutely exposed to temperature variation. Furthermore, we established functional links between cardiac plasticity, metabolic performance, and thermal tolerance, providing evidence that plasticity in cardiac capacity may be one mechanism for coping with climate change.

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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Junho, Eom; Chris M, Wood;

    Abstract Ammonia is both a respiratory gas and a toxicant in teleost fish. Hyperventilation is a well-known response to elevations of both external and internal ammonia levels. Branchial neuroepithelial cells (NECs) are thought to serve as internal sensors of plasma ammonia (peripheral chemoreceptors), but little is known about other possible ammonia-sensors. Here, we investigated whether trout possess external sensors and/or internal central chemoreceptors for ammonia. For external sensors, we analyzed the time course of ventilatory changes at the start of exposure to high environmental ammonia (HEA, 1 mM). Hyperventilation developed gradually over 20 min, suggesting that it was a response to internal ammonia elevation. We also directly perfused ammonia solutions (0.01–1 mM) to the external surfaces of the first gill arches. Immediate hypoventilation occurred. For central chemoreceptors, we injected ammonia solutions (0.5–1.0 mM) directly onto the surface of the hindbrain of anesthetized trout. Immediate hyperventilation occurred. This is the first evidence of central chemoreception in teleost fish. We conclude that trout possess both external ammonia sensors, and dual internal ammonia sensors (perhaps for redundancy), but their roles differ. External sensors cause short term hypoventilation, which would help limit toxic waterborne ammonia uptake. When fish cannot avoid HEA, the diffusion of waterborne ammonia into the blood will stimulate both peripheral (NECs) and central (brain) chemoreceptors, resulting in hyperventilation. This hyperventilation will be beneficial in increasing ammonia excretion via the Rh metabolon system in the gills not only after HEA exposure, but also after endogenous ammonia loading from feeding or exercise.

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    Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology
    Article . 2021 . Peer-reviewed
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      Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology
      Article . 2021 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Diego Robledo; Juan A. Rubiolo; Santiago Cabaleiro; Paulino Martínez; +1 Authors

    Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates This work was funded by Spanish Ministry of Economy and Competitiveness and European Regional Development Funds (AGL2012-35904), Ministry of Science and Innovation (Consolider Ingenio, Aquagenomics, CSD2007-00002), and Local Government. Xunta de Galicia (GRC2014/010). DR was supported by a FPU fellowship funded by Spanish Ministry of Education, Culture and Sport (AP2012-0254) and a postdoctoral contract funded by the Biotechnology and Biological Science Research Council (BBSRC) grant BB/N024044/1 SI

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    Scientific Reports
    Article . 2017 . Peer-reviewed
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    Authors: Fred D. Chibwana; Isabel Blasco-Costa; Simona Georgieva; Ken M. Hosea; +3 Authors

    Abstract Diplostomid trematodes comprise a large and diverse group of widespread digeneans whose larval stages are important parasitic pathogens that may exert serious impacts in wild and cultured freshwater fish. However, our understanding of their diversity remains incomplete especially in the tropics. Our study is the first application of a DNA-based approach to diplostomid diversity in the African continent by generating a database linking sequences for the mitochondrial cytochrome c oxidase subunit 1 (cox1) barcode region and ITS1-5.8S-ITS2 rRNA gene cluster for brain-infecting diplostomid metacercariae from the catfish Clarias gariepinus. Analyses of newly-generated partial cox1 sequences for 34 larval isolates of Tylodelphys spp. from Tanzania and Diplostomum spp. from Tanzania and Nigeria revealed three strongly supported reciprocally monophyletic lineages of Tylodelphys spp. and one of an unknown species of Diplostomum. The average intraspecific divergence for the cox1 sequences for each recognised novel lineage was distinctly lower compared with interspecific divergence (0.46–0.75% vs 11.7–14.8%). The phylogenetic hypotheses estimated from Bayesian inference and maximum likelihood analyses of ITS1-5.8S-ITS2 data exhibited congruent strong support for the cox1-derived lineages. Our study thus provides molecular-based evidence for the existence of three distinct brain-infecting species co-occurring in natural populations of C. gariepinus. Based on phylogenetic analyses, we re-allocated Diplostomum mashonense Beverley-Burton (1963) to the genus Tylodelphys as a new combination. We also generated cox1 and ITS1-5.8S-ITS2 sequences for an unknown species of Diplostomum from another African fish host, Synodontis nigrita.

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    Infection, Genetics and Evolution
    Other literature type . Article . 2013 . Peer-reviewed
    License: Elsevier TDM
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      Infection, Genetics and Evolution
      Other literature type . Article . 2013 . Peer-reviewed
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    Authors: Mélanie Debiais-Thibaud; Cushla J. Metcalfe; Jacob Pollack; Isabelle Germon; +5 Authors

    Background: The Dlx gene family encodes transcription factors involved in the development of a wide variety of morphological innovations that first evolved at the origins of vertebrates or of the jawed vertebrates. This gene family expanded with the two rounds of genome duplications that occurred before jawed vertebrates diversified. It includes at least three bigene pairs sharing conserved regulatory sequences in tetrapods and teleost fish, but has been only partially characterized in chondrichthyans, the third major group of jawed vertebrates. Here we take advantage of developmental and molecular tools applied to the shark Scyliorhinus canicula to fill in the gap and provide an overview of the evolution of the Dlx family in the jawed vertebrates. These results are analyzed in the theoretical framework of the DDC (Duplication-Degeneration-Complementation) model.Results: The genomic organisation of the catshark Dlx genes is similar to that previously described for tetrapods. Conserved non-coding elements identified in bony fish were also identified in catshark Dlx clusters and showed regulatory activity in transgenic zebrafish. Gene expression patterns in the catshark showed that there are some expression sites with high conservation of the expressed paralog(s) and other expression sites with events of paralog sub-functionalization during jawed vertebrate diversification, resulting in a wide variety of evolutionary scenarios within this gene family.Conclusion: Dlx gene expression patterns in the catshark show that there has been little neo-functionalization in Dlx genes over gnathostome evolution. In most cases, one tandem duplication and two rounds of vertebrate genome duplication have led to at least six Dlx coding sequences with redundant expression patterns followed by some instances of paralog sub-functionalization. Regulatory constraints such as shared enhancers, and functional constraints including gene pleiotropy, may have contributed to the evolutionary inertia leading to high redundancy between gene expression patterns. International audience

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    Authors: López-Barneo, J; Nurse, C A; Nilsson, G E; Buck, L T; +2 Authors

    Survival success under conditions of acute oxygen deprivation depends on efficiency of the central and peripheral chemoreception, optimization of oxygen extraction from the hypoxic environment and its delivery to the periphery, and adjustments of energy production and consumption. This article uses a comparative approach to assess the efficiency of adaptive strategies used by anoxia-tolerant and hypoxia-sensitive species to support survival during the first minutes to 1 h of oxygen deprivation. An aquatic environment is much more demanding in terms of diurnal and seasonal variations of the ambient oxygen availability from anoxia to hyperoxia than is an air environment. Therefore, fishes and aquatic turtles have developed a number of adaptive responses, which are lacking in most of the terrestrial mammals, to cope with these extreme conditions. These include efficient central and peripheral chemoreception, acute changes in respiratory rate and amplitude, and acute increase of the gas-exchange interface. A special set of adaptive mechanisms are engaged in reduction of the energy expenditure of the major oxygen-consuming organs: the brain and the heart. Both reduction of ATP consumption and a switch to alterative energy sources contribute to the maintenance of ATP and ion balance in hypoxia-tolerant animals. Hypoxia and hyperoxia are conditions favoring development of oxidative stress. Efficient protection from oxidation in anoxia-tolerant species includes reduction in the glutamate levels in the brain, stabilization of the mitochondrial function, and maintenance of nitric oxide production under conditions of oxygen deprivation. We give an overview of the current state of knowledge on some selected molecular and cellular acute adaptive mechanisms. These include the mechanisms of chemoreception in adult and neonatal mammals and in fishes, acute metabolic adaptive responses in the brain, and the role of nitrite in the preservation of heart function under hypoxic conditions.

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    Physiological and Biochemical Zoology
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