@article {9903, title = {Settlement patterns and temporal successions of coral reef cryptic communities affect diversity assessments using autonomous reef monitoring structures (ARMS).}, journal = {Sci Rep}, volume = {14}, year = {2024}, month = {2024 Nov 07}, pages = {27061}, abstract = {

Autonomous Reef Monitoring Structures (ARMS) are used worldwide to assess cryptic diversity, especially on coral reefs. They were developed as standardised tools, yet conditions of deployment, such as immersion duration and/or deployment and retrieval seasons, vary among studies. Here we studied temporal and seasonal variability in coral reef cryptic communities sampled with 15 ARMS on a single coral reef slope site at Reunion Island, Southwest Indian Ocean. Settlement patterns and temporal succession of Eukaryote communities were investigated across three immersion times (6\ months, 1\ year, 2\ years), two immersion seasons (hot vs. cool) and three fractions (500-2000\ μm, 106-500\ μm, sessile) using two genetic markers (18S, COI). Both markers detected different taxa with different resolutions, but broadly similar patterns of community composition and structure. While OTU diversity of communities did not change with immersion time and season, these parameters significantly affected community structure and composition. Our results showed a decrease of the similarity of ARMS communities with duration of immersion, and a strong temporal turnover of species with only a small proportion of the diversity persisting over time. The small proportion of OTUs assigned at phylum level highlights the uniqueness of the Mascarene cryptobiome.

}, keywords = {Animals, Anthozoa, Biodiversity, Coral Reefs, Environmental Monitoring, Indian Ocean, Seasons}, issn = {2045-2322}, doi = {10.1038/s41598-024-76834-8}, author = {Cou{\"e}del, Marion and Dettai, Agn{\`e}s and Mireille M.M. Guillaume and Bonillo, C{\'e}line and Baptiste Frattini and Bruggemann, J Henrich} } @article {8728, title = {Exploration of chemosensory ionotropic receptors in cephalopods: the IR25 gene is expressed in the olfactory organs, suckers, and fins of Sepia officinalis.}, journal = {Chem Senses}, volume = {46}, year = {2021}, month = {2021 01 01}, abstract = {

While they are mostly renowned for their visual capacities, cephalopods are also good at olfaction for prey, predator, and conspecific detection. The olfactory organs and olfactory cells are well described but olfactory receptors-genes and proteins-are still undescribed in cephalopods. We conducted a broad phylogenetic analysis of the ionotropic glutamate receptor family in mollusks (iGluR), especially to identify IR members (Ionotropic Receptors), a variant subfamily whose involvement in chemosensory functions has been shown in most studied protostomes. A total of 312 iGluRs sequences (including 111 IRs) from gastropods, bivalves, and cephalopods were identified and annotated. One orthologue of the gene coding for the chemosensory IR25 co-receptor has been found in Sepia officinalis (Soff-IR25). We searched for Soff-IR25 expression at the cellular level by in situ hybridization in whole embryos at late stages before hatching. Expression was observed in the olfactory organs, which strongly validates the chemosensory function of this receptor in cephalopods. Soff-IR25 was also detected in the developing suckers, which suggests that the unique {\guillemotleft} taste by touch {\guillemotright} behavior that cephalopods execute with their arms and suckers share features with olfaction. Finally, Soff-IR25 positive cells were unexpectedly found in fins, the two posterior appendages of cephalopods, mostly involved in locomotory functions. This result opens new avenues of investigation to confirm fins as additional chemosensory organs in cephalopods.

}, keywords = {Animals, Cephalopoda, Phylogeny, Receptors, Ionotropic Glutamate, Receptors, Odorant, Sepia, Smell}, issn = {1464-3553}, doi = {10.1093/chemse/bjab047}, author = {Aude Andouche and Valera, St{\'e}phane and S{\'e}bastien Baratte} } @article {8133, title = {Gonadal transcriptomes associated with sex phenotypes provide potential male and female candidate genes of sex determination or early differentiation in Crassostrea gigas, a sequential hermaphrodite mollusc.}, journal = {BMC Genomics}, volume = {22}, year = {2021}, month = {2021 Aug 09}, pages = {609}, abstract = {

BACKGROUND: In the animal kingdom, mollusca is an important phylum of the Lophotrochozoa. However, few studies have investigated the molecular cascade of sex determination/early gonadal differentiation within this phylum. The oyster Crassostrea gigas is a sequential irregular hermaphrodite mollusc of economic, physiological and phylogenetic importance. Although some studies identified genes of its sex-determining/-differentiating pathway, this particular topic remains to be further deepened, in particular with regard to the expression patterns. Indeed, these patterns need to cover the entire period of sex lability and have to be associated to future sex phenotypes, usually impossible to establish in this sequential hermaphrodite. This is why we performed a gonadal RNA-Seq analysis of diploid male and female oysters that have not changed sex for 4 years, sampled during the entire time-window of sex determination/early sex differentiation (stages 0 and 3 of the gametogenetic cycle). This individual long-term monitoring gave us the opportunity to explain the molecular expression patterns in the light of the most statistically likely future sex of each oyster.

RESULTS: The differential gene expression analysis of gonadal transcriptomes revealed that 9723 genes were differentially expressed between gametogenetic stages, and 141 between sexes (98 and 43 genes highly expressed in females and males, respectively). Eighty-four genes were both stage- and sex-specific, 57 of them being highly expressed at the time of sex determination/early sex differentiation. These 4 novel genes including Trophoblast glycoprotein-like, Protein PML-like, Protein singed-like and PREDICTED: paramyosin, while being supported by RT-qPCR, displayed sexually dimorphic gene expression patterns.

CONCLUSIONS: This gonadal transcriptome analysis, the first one associated with sex phenotypes in C. gigas, revealed 57 genes highly expressed in stage 0 or 3 of gametogenesis and which could be linked to the future sex of the individuals. While further study will be needed to suggest a role for these factors, some could certainly be original potential actors involved in sex determination/early sex differentiation, like paramyosin and could be used to predict the future sex of oysters.

}, keywords = {Animals, Crassostrea, Female, Gene Expression Profiling, Gonads, Humans, Male, Phenotype, Phylogeny, Sex Differentiation, Transcriptome}, issn = {1471-2164}, doi = {10.1186/s12864-021-07838-1}, author = {Broquard, Coralie and Saowaros, Suwansa-Ard and Lepoittevin, M{\'e}lanie and Degremont, Lionel and Lamy, Jean-Baptiste and Morga, Benjamin and Elizur, Abigail and Anne-Sophie Martinez} } @article {9730, title = {Not Frozen in the Ice: Large and Dynamic Rearrangements in the Mitochondrial Genomes of the Antarctic Fish}, journal = {Genome Biology and Evolution}, volume = {13}, year = {2021}, month = {2021 Mar 01}, abstract = {

The vertebrate mitochondrial genomes generally present a typical gene order. Exceptions are uncommon and important to study the genetic mechanisms of gene order rearrangements and their consequences on phylogenetic output and mitochondrial function. Antarctic notothenioid fish carry some peculiar rearrangements of the mitochondrial gene order. In this first systematic study of 28 species, we analyzed known and undescribed mitochondrial genome rearrangements for a total of eight different gene orders within the notothenioid fish. Our reconstructions suggest that transpositions, duplications, and inversion of multiple genes are the most likely mechanisms of rearrangement in notothenioid mitochondrial genomes. In Trematominae, we documented an extremely rare inversion of a large genomic segment of 5,300 bp that partially affected the gene compositional bias but not the phylogenetic output. The genomic region delimited by nad5 and trnF, close to the area of the Control Region, was identified as the hot spot of variation in Antarctic fish mitochondrial genomes. Analyzing the sequence of several intergenic spacers and mapping the arrangements on a newly generated phylogeny showed that the entire history of the Antarctic notothenioids is characterized by multiple, relatively rapid, events of disruption of the gene order. We hypothesized that a pre-existing genomic flexibility of the ancestor of the Antarctic notothenioids may have generated a precondition for gene order rearrangement, and the pressure of purifying selection could have worked for a rapid restoration of the mitochondrial functionality and compactness after each event of rearrangement.

}, keywords = {Animals, Antarctic Regions, Evolution, Molecular, Fishes, Freezing, Gene Order, Gene Rearrangement, Genes, Mitochondrial, Genome, Mitochondrial, Genomics, Ice, Models, Genetic, Phylogeny, Vertebrates}, issn = {1759-6653}, doi = {10.1093/gbe/evab017}, url = {https://doi.org/10.1093/gbe/evab017}, author = {Papetti, Chiara and Babbucci, Massimiliano and Dettai, Agn{\`e}s and Basso, Andrea and Lucassen, Magnus and Harms, Lars and C{\'e}line Bonillo and Heindler, Franz Maximilian and Patarnello, Tomaso and Negrisolo, Enrico} } @article {9732, title = {Raising names from the dead: A time-calibrated phylogeny of frog shells (Bursidae, Tonnoidea, Gastropoda) using mitogenomic data.}, journal = {Mol Phylogenet Evol}, volume = {156}, year = {2021}, month = {2021 Mar}, pages = {107040}, abstract = {

With 59 Recent species, Bursidae, known as {\guillemotleft}frog shells{\guillemotright}, are a small but widely distributed group of tropical and subtropical gastropods that are most diverse in the Indo-West Pacific. The present study is aimed at reconstructing phylogenetic relationships of bursid gastropods based on extensive and representative taxon sampling. Five genetic markers (cytochrome c oxidase subunit I (cox1), 16\ s and 12\ s rRNA mitochondrial genes, 28\ s rRNA and Histone H3 nuclear gene) were sequenced for over 30 species in every known genus but Crossata. Furthermore, we sequenced the complete mt-genome of 9 species (10 specimens) (Aspa marginata, Marsupina bufo, Korrigania quirihorai, Korrigania fijiensis, Tutufa rubeta, Bursa lamarckii, Lampasopsis rhodostoma (twice), Bufonaria perelegans and Bursa aff. tuberosissima). Our analysis recovered Bursidae as a monophyletic group, whereas the genus Bursa was found to be polyphyletic. The genera Talisman and Dulcerana are resurrected and the genera Alanbeuella gen. nov. and Korrigania gen. nov. are described. Dating analysis using 21 extinct taxa for node and simplified tip calibrations was performed, showing a diversification of the group in two phases. Diversification may be linked to tectonic events leading to biodiversity relocation from the western Tethys toward the Indo-Pacific.

}, keywords = {Animals, Bayes Theorem, Calibration, Fossils, Gastropoda, Genes, Mitochondrial, Genome, Mitochondrial, Phylogeny, Sequence Analysis, DNA, Time Factors}, issn = {1095-9513}, doi = {10.1016/j.ympev.2020.107040}, author = {Sanders, Malcolm T and Merle, Didier and Laurin, Michel and C{\'e}line Bonillo and Puillandre, Nicolas} } @article {6665, title = {Digestive enzyme ratios are good indicators of hatchling yolk reserve and digestive gland maturation in early life stages of cuttlefish Sepia officinalis L.: application of these new tools in ecology and aquaculture}, journal = {Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology}, volume = {188}, year = {2018}, pages = {57-76}, abstract = {In Sepia officinalis (Linnaeus, 1758), the digestive gland matures during the first month post-hatching, while a shift from intracellular acid to extracellular alkaline digestion occurs. The purpose of this study was to investigate the possibility of using enzymatic ratios for the description of digestive system maturation in early life stages of S. officinalis. Second, it is intended to apply these new tools as eco-physiological indicators for understanding the impact of cuttlefish eggs{\textquoteright} life history from different spawning sites of the English Channel on digestive performance of juveniles. An experimental rearing was performed over 35\ days after hatching (DAH) on juveniles from wild collected eggs in 2010 and 2011. Four digestive enzyme activities and their ratios [i.e., trypsin, cathepsin, acid (ACP), and alkaline (ALP) phosphatase, ALP/ACP, and trypsin/cathepsin] were studied along with histological features (e.g., internal yolk surface and digestive gland development). The two enzyme ratios were good indicators of digestive system maturation allowing the study of the digestive gland{\textquoteright}s development. They were highly correlated to juveniles{\textquoteright} weight increase and histological features of the gland in early DAH. These ratios described more accurately the shift occurring between the intracellular acid and the extracellular alkaline modes of digestion in S. officinalis and were more specific than separated enzyme activities. Their application as eco-physiological tools revealed that enzyme ratios reflected yolk content and digestive gland development in new hatching juveniles. Finally, ALP/ACP ratio was shown to be a powerful tool to describe growth performance of S. officinalis which is useful for aquaculture optimization. {\textcopyright} 2017, Springer-Verlag GmbH Germany.}, keywords = {Acid Phosphatase, alkaline phosphatase, anatomy and histology, animal, Animals, Aquaculture, cathepsin, Cathepsins, cuttlefish, Gastrointestinal Tract, Physiology, Sepia, Trypsin}, issn = {01741578}, doi = {10.1007/s00360-017-1115-4}, url = {https://link.springer.com/article/10.1007\%2Fs00360-017-1115-4}, author = {Safi, Georges and Anne-Sophie Martinez and Le Pabic, Charles and Estelle Le Bihan and Jean-Paul Robin and Koueta, Noussith{\'e}} } @article {6940, title = {Regulation of Extracellular Matrix Synthesis by Shell Extracts from the Marine Bivalve Pecten maximus in Human Articular Chondrocytes- Application for Cartilage Engineering.}, journal = {Mar Biotechnol (NY)}, volume = {20}, year = {2018}, month = {2018 Aug}, pages = {436-450}, abstract = {

The shells of the bivalve mollusks are organo-mineral structures predominantly composed of calcium carbonate, but also of a minor organic matrix, a mixture of proteins, glycoproteins, and polysaccharides. These proteins are involved in mineral deposition and, more generally, in the spatial organization of the shell crystallites in well-defined microstructures. In this work, we extracted different organic shell extracts (acid-soluble matrix, acid-insoluble matrix, water-soluble matrix, guanidine HCl/EDTA-extracted matrix, referred as ASM, AIM, WSM, and EDTAM, respectively) from the shell of the scallop Pecten maximus and studied their biological activities on human articular chondrocytes (HACs). We found that these extracts differentially modulate the biological activities of HACs, depending on the type of extraction and the concentration used. Furthermore, we showed that, unlike ASM and AIM, WSM promotes maintenance of the chondrocyte phenotype in monolayer culture. WSM increased the expression of chondrocyte-specific markers (aggrecan and type II collagen), without enhancing that of the main chondrocyte dedifferentiation marker (type I collagen). We also demonstrated that WSM could favor redifferentiation of chondrocyte in collagen sponge scaffold in hypoxia. Thus, this study suggests that the organic matrix of Pecten maximus, particularly WSM, may contain interesting molecules with chondrogenic effects. Our research emphasizes the potential use of WSM of Pecten maximus for cell therapy of cartilage.

}, keywords = {Aged, Aged, 80 and over, Aggrecans, Animal Shells, Animals, Cell Differentiation, Cells, Cultured, Chondrocytes, Collagen Type II, Extracellular Matrix, Gene Expression Profiling, Humans, Middle Aged, Pecten, Phenotype}, issn = {1436-2236}, doi = {10.1007/s10126-018-9807-7}, author = {Bouyoucef, Mouloud and Rakic, Rodolphe and G{\'o}mez-Leduc, Tangni and Latire, Thomas and Marin, Fr{\'e}d{\'e}ric and Leclercq, Sylvain and Carreiras, Franck and Antoine Serpentini and Lebel, Jean-Marc and Gal{\'e}ra, Philippe and Legendre, Florence} } @article {4419, title = {GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.}, journal = {BMC Bioinformatics}, volume = {16}, year = {2015}, month = {2015}, pages = {401}, abstract = {

BACKGROUND: The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database.

DESCRIPTION: We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries.

CONCLUSIONS: The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.

}, keywords = {Animals, Base Sequence, Computational Biology, Crassostrea, Databases, Genetic, Gene Library, Gene Ontology, Genome, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Sequence Analysis, RNA, Software, Transcriptome}, issn = {1471-2105}, doi = {10.1186/s12859-015-0833-4}, author = {Guillaume Rivi{\`e}re and Klopp, Christophe and Ibouniyamine, Nabihoudine and Huvet, Arnaud and Boudry, Pierre and Pascal Favrel} } @article {4418, title = {Regulation of Hox orthologues in the oyster Crassostrea gigas evidences a functional role for promoter DNA methylation in an invertebrate.}, journal = {FEBS Lett}, volume = {589}, year = {2015}, month = {2015 Jun 4}, pages = {1459-66}, abstract = {

DNA methylation within promoter regions (PRDM) controls vertebrate early gene transcription and thereby development, but is neglected outside this group. However, epigenetic features in the oyster Crassostrea gigas suggest functional significance of PDRM in invertebrates. To investigate this, reporter constructs containing in vitro methylated oyster Hox gene promoters were transfected into oyster embryos. The influence of in vivo methylation was studied using bisulfite sequencing and DNA methyltransferase inhibition during development. Our results demonstrate that methylation controls the transcriptional activity of the promoters investigated, unraveling a functional role for PRDM in a lophotrochozoan, an important finding regarding the evolution of epigenetic regulation.

}, keywords = {Animals, Azacitidine, CHO Cells, Crassostrea, Cricetinae, Cricetulus, DNA (Cytosine-5-)-Methyltransferase, DNA Methylation, Embryo, Nonmammalian, Enzyme Inhibitors, Gene Expression Regulation, Developmental, Homeodomain Proteins, Invertebrates, Promoter Regions, Genetic, Transfection}, issn = {1873-3468}, doi = {10.1016/j.febslet.2015.04.043}, author = {Saint-Carlier, Emma and Guillaume Rivi{\`e}re} } @article {3510, title = {Acute toxicity of 8 antidepressants: what are their modes of action?}, journal = {Chemosphere}, volume = {108}, year = {2014}, month = {2014 Aug}, pages = {314-9}, abstract = {

Currently, the hazard posed by pharmaceutical residues is a major concern of ecotoxicology. Most of the antidepressants belong to a family named the Cationic Amphipathic Drugs known to have specific interactions with cell membranes. The present study assessed the impact of eight antidepressants belonging to selective serotonin reuptake inhibitors or serotonin norepinephrine reuptake inhibitors by the combination of multi-approaches (in vivo, in vitro, in silico) and gives some insights on the mode of action for these molecules. Antidepressants were from the most to the least toxic compound for Daphnia magna: Sertraline (EC50=1.15 mg L(-1))\>Clomipramine (2.74 mg L(-1))\>Amitriptyline (4.82 mg L(-1))\>Fluoxetine (5.91 mg L(-1))\>Paroxetine (6.24 mg L(-1))\>Mianserine (7.81 mg L(-1))\>Citalopram (30.14 mg L(-1)) and Venlafaxine (141.28 mg L(-1)). These acute toxicities were found correlated to Log Kow coefficients (R=0.93, p\<0.001) and to cytotoxicity assessed on abalone hemocytes through the neutral red uptake assay (R=0.96, p\<0.001). If narcosis as mode of action is typically expected during acute ecotoxicity bioassays, we showed by molecular modeling that particular interactions can exist between antidepressants and phosphatidylcholine, a major component of cell membranes, leading to a more specific mode of action corresponding to a potential acidic hydrolysis of ester functions.

}, keywords = {Animals, Antidepressive Agents, Cell Survival, Cells, Cultured, Daphnia, Environmental Pollutants, Gastropoda, Hemocytes, Lysosomes, Models, Molecular, Phosphatidylcholines, Serotonin Uptake Inhibitors}, issn = {1879-1298}, doi = {10.1016/j.chemosphere.2014.01.057}, author = {Minguez, Laetitia and Farcy, E and Ballandonne, C{\'e}line and Lepailleur, Alban and Antoine Serpentini and Jean-Marc Lebel and Bureau, Ronan and Halm-Lemeille, Marie-Pierre} } @article {3512, title = {Assessment of cytotoxic and immunomodulatory properties of four antidepressants on primary cultures of abalone hemocytes (Haliotis tuberculata).}, journal = {Aquat Toxicol}, volume = {153}, year = {2014}, month = {2014 Aug}, pages = {3-11}, abstract = {

Pharmaceutical compounds like antidepressants found in surface waters raise concerns due to their potential toxicity on non-target aquatic organisms. This study aimed at investigating the in vitro cytotoxicity and immunomodulatory properties of four common antidepressants, namely Amitriptyline, Clomipramine, Citalopram and Paroxetine, on primary cultures of abalone hemocytes (Haliotis tuberculata), after 48 h-exposure. Effects on immunocompetence (phagocytosis, levels of reactive oxygen species, esterase activity and lysosomal membrane destabilization) were assessed. Results obtained by MTT assays revealed that acute toxicity is unlikely to occur in the environment since the LC50s of the four antidepressants are at the mg/L level. The different immunological endpoints displayed a biphasic response, with an increase at the lowest concentration (i.e. 1 μg/L) followed by a decrease at higher concentrations. Overall, Amitriptyline and Clomipramine, the two tricyclic antidepressants, had higher immunomodulatory capacities than the two selective serotonin reuptake inhibitors Citalopram and Paroxetine. Amitriptyline was the most potent and Citalopram the least potent drug in altering immune function in H. tuberculata.

}, keywords = {Animals, Antidepressive Agents, Cell Survival, Cells, Cultured, Enzyme Activation, Esterases, Gastropoda, Hemocytes, Immunity, Innate, Lethal Dose 50, Phagocytosis, Reactive Oxygen Species, Water Pollutants, Chemical}, issn = {1879-1514}, doi = {10.1016/j.aquatox.2013.10.020}, author = {Minguez, Laetitia and Halm-Lemeille, Marie-Pierre and Katherine Costil and Bureau, Ronan and Jean-Marc Lebel and Antoine Serpentini} } @article {3701, title = {Direct evidence for maternal inheritance of bacterial symbionts in small deep-sea clams (Bivalvia: Vesicomyidae).}, journal = {Naturwissenschaften}, volume = {101}, year = {2014}, month = {2014 May}, pages = {373-83}, abstract = {

Bacterial symbiont transmission is a key step in the renewal of the symbiotic interaction at each host generation, and different modes of transmission can be distinguished. Vesicomyidae are chemosynthetic bivalves from reducing habitats that rely on symbiosis with sulfur-oxidizing bacteria, in which two studies suggesting vertical transmission of symbionts have been published, both limited by the imaging techniques used. Using fluorescence in situ hybridization and transmission electron microscopy, we demonstrate that bacterial symbionts of Isorropodon bigoti, a gonochoristic Vesicomyidae from the Guiness cold seep site, occur intracellularly within female gametes at all stages of gametogenesis from germ cells to mature oocytes and in early postlarval stage. Symbionts are completely absent from the male gonad and gametes. This study confirms the transovarial transmission of symbionts in Vesicomyidae and extends it to the smaller species for which no data were previously available.

}, keywords = {Animals, Bacterial Physiological Phenomena, Bivalvia, Female, Germ Cells, Gonads, In Situ Hybridization, Fluorescence, Male, Microscopy, Electron, Transmission, Oceans and Seas, Symbiosis}, issn = {1432-1904}, doi = {10.1007/s00114-014-1165-3}, author = {Szafranski, Kamil M and Sylvie M Gaudron and S{\'e}bastien Duperron} } @article {4126, title = {Diversity of cultivable fungi associated with Antarctic marine sponges and screening for their antimicrobial, antitumoral and antioxidant potential.}, journal = {World J Microbiol Biotechnol}, volume = {30}, year = {2014}, month = {2014 Jan}, pages = {65-76}, abstract = {

The diversity of sponge-associated fungi has been poorly investigated in remote geographical areas like Antarctica. In this study, 101 phenotypically different fungal isolates were obtained from 11 sponge samples collected in King George Island, Antarctica. The analysis of ITS sequences revealed that they belong to the phylum Ascomycota. Sixty-five isolates belong to the genera Geomyces, Penicillium, Epicoccum, Pseudeurotium, Thelebolus, Cladosporium, Aspergillus, Aureobasidium, Phoma, and Trichocladium but 36 isolates could not be identified at genus level. In order to estimate the potential of these isolates as producers of interesting bioactivities, antimicrobial, antitumoral and antioxidant activities of fungal culture extracts were assayed. Around 51\% of the extracts, mainly from the genus Geomyces and non identified relatives, showed antimicrobial activity against some of the bacteria tested. On the other hand, around 42\% of the extracts showed potent antitumoral activity, Geomyces sp. having the best performance. Finally, the potential of the isolated fungi as producers of antioxidant activity seems to be moderate. Our results suggest that fungi associated with Antarctic sponges, particularly Geomyces, would be valuable sources of antimicrobial and antitumoral compounds. To our knowledge, this is the first report describing the biodiversity and the metabolic potential of fungi associated with Antarctic marine sponges.

}, keywords = {Animals, Antarctic Regions, Anti-Bacterial Agents, Antineoplastic Agents, Antioxidants, Ascomycota, DNA, Ribosomal Spacer, Porifera, Sequence Analysis, DNA}, issn = {1573-0972}, doi = {10.1007/s11274-013-1418-x}, author = {Henr{\'\i}quez, Marlene and Vergara, Karen and Norambuena, Javiera and Beiza, Andrea and Maza, Felipe and Ubilla, Pamela and Araya, Ivanna and Ch{\'a}vez, Renato and San-Mart{\'\i}n, Aurelio and Darias, Jos{\'e} and Darias, Maria and Vaca, Inmaculada} } @article {3509, title = {The effect of different polychlorinated biphenyls on two aquatic models, the green alga Pseudokirchneriella subcapitata and the haemocytes from the European abalone Haliotis tuberculata.}, journal = {Chemosphere}, volume = {110}, year = {2014}, month = {2014 Sep}, pages = {120-8}, abstract = {

The present study was conducted to determine the toxicity of different polychlorinated biphenyls (PCBs) on the green algae, Pseudokirchneriella subcapitata and the haemocytes from the European abalone, Haliotis tuberculata. Using the algal growth inhibition test, the green algae median Effective Concentration (EC50) values ranged from 0.34μM for PCB28 to more than 100μM for PCBs 101 and 153. Considering the MTT viability test, the abalone EC50 values ranged from 1.67μM for PCB153 to 89μM for PCB28. Our results in contrast to previous observation in vertebrates did not show significant differences between the dioxin like- and non dioxin like-PCBs toxicities regardless of the model used. However, our results demonstrated that the toxicities of PCBs were species dependent. For example, PCB28 was the most toxic compound for P. subcapitata whereas PCBs 1, 180 and 153 were less toxic for that species. On the contrary, PCB153 was reported as the most toxic for H. tuberculata haemocytes and PCB28 the least toxic. To investigate the mode of action of these compounds, we used an in silico method. Our results suggested that PCBs have a non-specific mode of action (e.g., narcosis) on green algae, and another mode of action, probably more specific than narcosis, was reported for PCBs on the abalone haemocytes.

}, keywords = {Animals, Chlorophyta, Environmental Pollutants, Gastropoda, Hemocytes, Polychlorinated Biphenyls, Tetrachlorodibenzodioxin}, issn = {1879-1298}, doi = {10.1016/j.chemosphere.2014.02.023}, author = {Halm-Lemeille, Marie-Pierre and Abbaszadeh Fard, Elham and Latire, T and Ferard, Jean-Fran{\c c}ois and Katherine Costil and Jean-Marc Lebel and Bureau, Ronan and Antoine Serpentini} } @article {3511, title = {Effects of acute exposures to mecoprop, mecoprop-p and their biodegradation product (2-MCP) on the larval stages of the Pacific oyster, Crassostrea gigas.}, journal = {Aquat Toxicol}, volume = {146}, year = {2014}, month = {2014 Jan}, pages = {165-75}, abstract = {

Studies have shown that pesticides are sometimes detected at rather high levels in seawater and it has been suggested that these chemical compounds could act as additional stress factor for oysters cultured in coastal environments. The effects of pesticides on marine molluscs could be particularly harmful in the early stages which correspond to critical life stages. This study aimed to assess the effects of mecoprop, mecoprop-p and their degradation compound 2-methyl-4-chlorophenol on two larval stages of Crassostrea gigas. Embryotoxic effects were assessed on veliger larvae after 36 h exposures, and both percentages of normal larvae and types of abnormalities were taken into account. The effects of the three substances were evaluated on 21-day-old pediveliger larvae by calculating metamorphosis rates after 24h exposures. The results of the embryotoxicity assay indicated that 2-methyl-4-chlorophenol was more toxic (EC50: 10.81 mg L(-1)) than its parent compounds (EC50 mecoprop: 42.55 mg L(-1); EC50 mecoprop-p: 78.85 mg L(-1)). Mecoprop in particular injured shell formation with an increase of shell abnormalities following herbicide concentrations. The active substances were not toxic to metamorphosis processes, but 2-MCP was revealed to be more toxic to the success of metamorphosis (EC50: 7.20 mg L(-1)) than to embryo-larval development. However, the toxic concentrations were several orders of magnitude higher than environmental concentrations.

}, keywords = {2-Methyl-4-chlorophenoxyacetic Acid, Animals, Chlorophenols, Crassostrea, Embryo, Nonmammalian, Larva, Metamorphosis, Biological, Water Pollutants, Chemical}, issn = {1879-1514}, doi = {10.1016/j.aquatox.2013.11.008}, author = {Mottier, A and Kientz-Bouchart, Val{\'e}rie and Dubreule, Christelle and Antoine Serpentini and Jean-Marc Lebel and Katherine Costil} } @article {3252, title = {Global imprint of historical connectivity on freshwater fish biodiversity.}, journal = {Ecol Lett}, volume = {17}, year = {2014}, month = {2014 Sep}, pages = {1130-40}, abstract = {

The relative importance of contemporary and historical processes is central for understanding biodiversity patterns. While several studies show that past conditions can partly explain the current biodiversity patterns, the role of history remains elusive. We reconstructed palaeo-drainage basins under lower sea level conditions (Last Glacial Maximum) to test whether the historical connectivity between basins left an imprint on the global patterns of freshwater fish biodiversity. After controlling for contemporary and past environmental conditions, we found that palaeo-connected basins displayed greater species richness but lower levels of endemism and beta diversity than did palaeo-disconnected basins. Palaeo-connected basins exhibited shallower distance decay of compositional similarity, suggesting that palaeo-river connections favoured the exchange of fish species. Finally, we found that a longer period of palaeo-connection resulted in lower levels of beta diversity. These findings reveal the first unambiguous results of the role played by history in explaining the global contemporary patterns of biodiversity.

}, keywords = {Animals, Biodiversity, Environment, Fishes, Fresh Water, Models, Biological}, issn = {1461-0248}, doi = {10.1111/ele.12319}, author = {Dias, Murilo S and Thierry Oberdorff and Bernard Hugueny and Leprieur, Fabien and J{\'e}z{\'e}quel, C{\'e}line and Cornu, Jean-Fran{\c c}ois and Brosse, S{\'e}bastien and Grenouillet, Gael and Pablo Tedesco} } @article {3394, title = {The Jumonji gene family in Crassostrea gigas suggests evolutionary conservation of Jmj-C histone demethylases orthologues in the oyster gametogenesis and development.}, journal = {Gene}, volume = {538}, year = {2014}, month = {2014 Mar 15}, pages = {164-75}, abstract = {

Jumonji (Jmj) proteins are histone demethylases, which control the identity of stem cells. Jmj genes were characterized from plants to mammals where they have been implicated in the epigenetic regulation of development. Despite the Pacific oyster Crassostrea gigas representing one of the most important aquaculture resources worldwide, the molecular mechanisms governing the embryogenesis and reproduction of this lophotrochozoan species remain poorly understood. However, annotations in the C. gigas EST library suggested the presence of putative Jumonji genes, raising the question of the conservation of this family of histone demethylases in the oyster. Using Primer walking, 5{\textquoteright}-RACE PCR and in silico analyses, we characterized nine Jumonji orthologues in the oyster, called Cg-Jmj, bearing conserved domains critical for putative histone demethylase activity. Phylogenic analyses revealed that oyster Jumonji cluster into two distinct groups: {\textquoteright}single-domain Jmj{\textquoteright} and {\textquoteright}multi-domain Jmj{\textquoteright}, and define 8 subgroups corresponding to each cognate orthologues in metazoans. RT-qPCR investigations showed specific regulations of Cg-Jmj mRNAs during the early development and along the reproduction cycle. Furthermore, in situ and in toto hybridizations indicate that oyster Jumonji genes are transcribed mostly within the gonad in adult oysters whereas they display a ubiquitous expression during embryonic and larval development. Our study demonstrates the presence of nine Jumonji orthologues in the oyster C. gigas. Their domain conservation and their expression profile suggest an implication during reproduction and development, questioning about the epigenetic regulation by histone methylation in lophotrochozoans.

}, keywords = {Animals, Base Sequence, Conserved Sequence, Crassostrea, Evolution, Molecular, Gametogenesis, Gene Expression Regulation, Developmental, Jumonji Domain-Containing Histone Demethylases, Molecular Sequence Data, Multigene Family, RNA, Messenger}, issn = {1879-0038}, doi = {10.1016/j.gene.2013.12.016}, author = {Alexandre Fellous and Pascal Favrel and Guo, Ximing and Guillaume Rivi{\`e}re} } @article {3631, title = {Looking for the bird Kiss: evolutionary scenario in sauropsids.}, journal = {BMC Evol Biol}, volume = {14}, year = {2014}, month = {2014}, pages = {30}, abstract = {

BACKGROUND: The neuropeptide Kiss and its receptor KissR are key-actors in the brain control of reproduction in mammals, where they are responsible for the stimulation of the activity of GnRH neurones. Investigation in other vertebrates revealed up to 3 Kiss and 4 KissR paralogs, originating from the two rounds of whole genome duplication in early vertebrates. In contrast, the absence of Kiss and KissR has been suggested in birds, as no homologs of these genes could be found in current genomic databases. This study aims at addressing the question of the existence, from an evolutionary perspective, of the Kisspeptin system in birds. It provides the first large-scale investigation of the Kisspeptin system in the sauropsid lineage, including ophidian, chelonian, crocodilian, and avian lineages.

RESULTS: Sauropsid Kiss and KissR genes were predicted from multiple genome and transcriptome databases by TBLASTN. Phylogenetic and syntenic analyses were performed to classify predicted sauropsid Kiss and KissR genes and to re-construct the evolutionary scenarios of both gene families across the sauropsid radiation.Genome search, phylogenetic and synteny analyses, demonstrated the presence of two Kiss genes (Kiss1 and Kiss2 types) and of two KissR genes (KissR1 and KissR4 types) in the sauropsid lineage. These four genes, also present in the mammalian lineage, would have been inherited from their common amniote ancestor. In contrast, synteny analyses supported that the other Kiss and KissR paralogs are missing in sauropsids as in mammals, indicating their absence in the amniote lineage. Among sauropsids, in the avian lineage, we demonstrated the existence of a Kiss2-like gene in three bird genomes. The divergence of these avian Kiss2-like sequences from those of other vertebrates, as well as their absence in the genomes of some other birds, revealed the processes of Kiss2 gene degeneration and loss in the avian lineage.

CONCLUSION: These findings contribute to trace back the evolutionary history of the Kisspeptin system in amniotes and sauropsids, and provide the first molecular evidence of the existence and fate of a Kiss gene in birds.

}, keywords = {Amino Acid Sequence, Animals, Avian Proteins, Biological Evolution, Birds, Humans, Kisspeptins, Molecular Sequence Data, Phylogeny, Receptors, G-Protein-Coupled, Reptiles, Sequence Alignment, Synteny}, issn = {1471-2148}, doi = {10.1186/1471-2148-14-30}, author = {Pasquier, J{\'e}r{\'e}my and Anne-Gaelle Lafont and Karine Rousseau and Qu{\'e}rat, Bruno and Chemineau, Philippe and Sylvie Dufour} } @article {4161, title = {A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): multiple invasions of intertidal habitats.}, journal = {Mol Phylogenet Evol}, volume = {70}, year = {2014}, month = {2014 Jan}, pages = {47-56}, abstract = {

The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies.

}, keywords = {Animals, Bayes Theorem, Ecosystem, Likelihood Functions, Perciformes, Phylogeny, Sequence Analysis, DNA}, issn = {1095-9513}, doi = {10.1016/j.ympev.2013.09.001}, author = {Hundt, Peter J and Samuel Iglesias and Hoey, Andrew S and Simons, Andrew M} } @article {3639, title = {Neuroendocrine gene expression reveals a decrease in dopamine D2B receptor with no changes in GnRH system during prepubertal metamorphosis of silvering in wild Japanese eel.}, journal = {Gen Comp Endocrinol}, volume = {206}, year = {2014}, month = {2014 Sep 15}, pages = {8-15}, abstract = {

Silvering is a prepubertal metamorphosis preparing the eel to the oceanic reproductive migration. A moderate gonad development occurs during this metamorphosis from the sedentary yellow stage to the migratory silver stage. The aim of this study was to elucidate the molecular aspects of various endocrine parameters of BPG axis at different ovarian developmental stages in wild yellow and silver female Japanese eels. The GSI of the sampled female eels ranged between 0.18 and 2.3\%, corresponding to yellow, pre-silver and silver stages. Gonad histology showed changes from previtellogenic oocytes in yellow eels to early vitellogenic oocytes in silver eels. Both serum E2 and T concentrations significantly increased with ovarian development indicating a significant activation of steroidogenesis during silvering. In agreement with previous studies, significant increases in pituitary gonadotropin beta subunits FSH-β and LH-β transcripts were also measured by qPCR, supporting that the activation of pituitary gonadotropin expression is likely responsible for the significant ovarian development observed during silvering. We investigated for the first time the possible brain neuroendocrine mechanisms involved in the activation of the pituitary gonadotropic function during silvering. By analyzing the expression of genes representative of the stimulatory GnRH control and the inhibitory dopaminergic control. The transcript levels of mGnRH and the three GnRH receptors did not change in the brain and pituitary between yellow and silver stages, suggesting that gene expression of the GnRH system is not significantly activated during silvering. The brain transcript levels of tyrosine hydroxylase, limiting enzyme of DA synthesis did not change during silvering, indicating that the DA synthesis activity was maintained. In contrast, a significant decrease in DA-D2B receptor expression in the forebrain and pituitary was observed, with no changes in DA-D2A receptor. The decrease in the pituitary expression of DA-D2BR during silvering would allow a reduced inhibitory effect of DA. We may raise the hypothesis that this regulation of D2BR gene expression is one of the neuroendocrine mechanisms involved in the slight activation of the pituitary gonadotropin and gonadal activity that occur at silvering.

}, keywords = {Animals, Cells, Cultured, Dopamine, Eels, Female, Follicle Stimulating Hormone, beta Subunit, Gene Expression Regulation, Gonadotropin-Releasing Hormone, Immunoblotting, Immunoenzyme Techniques, Luteinizing Hormone, beta Subunit, Metamorphosis, Biological, Neurosecretory Systems, Oocytes, Ovary, Real-Time Polymerase Chain Reaction, Receptors, Dopamine D2, Reproduction, Reverse Transcriptase Polymerase Chain Reaction, RNA, Messenger, Sexual Maturation, Skin Pigmentation}, issn = {1095-6840}, doi = {10.1016/j.ygcen.2014.08.001}, author = {Jeng, Shan-Ru and Wen-Shiun Yueh and Pen, Yi-Ting and Lee, Yan-Horn and Chen, Guan-Ru and Sylvie Dufour and Chang, Ching-Fong} } @article {3486, title = {New Sicydiinae phylogeny (Teleostei: Gobioidei) inferred from mitochondrial and nuclear genes: insights on systematics and ancestral areas.}, journal = {Mol Phylogenet Evol}, volume = {70}, year = {2014}, month = {2014 Jan}, pages = {260-71}, abstract = {

The Sicydiinae subfamily (Teleostei: Gobioidei) is the biggest contributor to the diversity of fish communities in river systems of tropical islands. These species are found in the Indo-Pacific area, the Caribbean region and West Africa. They spawn in freshwater, their planktotrophic larvae drift downstream to the sea where they develop, before returning to the rivers to grow and reproduce. Hence, they are called amphidromous. Their phylogeny has been explored using a total of 3545 sites from 5 molecular markers (mitochondrial DNA: 16S rDNA, cytochrome oxidase I, cytochrome b; nuclear DNA: rhodopsin gene and a nuclear marker specially developed for this study, the interferon regulatory factor 2 binding protein 1-IRF2PB1). Sequences were obtained for 59 Sicydiinae specimens of 9 known genera. The Bayesian and maximum likelihood analyses support the monophyly of the subfamily as well as the monophylyof all genera except Sicydium, which is paraphyletic. Five major clades were identified within this subfamily. One clade contained the genus Stiphodon. Another clade contained Sicyopterus, Sicydium and Parasicydium with Sicyopterus as sister genus of Sicydium. The non-monophyly of Sicydium subclade, because it includes the monotypic genus Parasicydium, challenged the validity of Parasicydium genus. Ancestral area reconstruction showed that the subfamily emerged in the Central West Pacific region implying that previous hypotheses proposing a dispersal route for Sicydiinae into the Atlantic Ocean are unsupported by the present analysis. Our results suggest that the hypotheses for the dispersal route of the genus Sicydium should be reconsidered.

}, keywords = {Animals, Bayes Theorem, Cell Nucleus, Cytochromes b, DNA, Mitochondrial, DNA, Ribosomal, Electron Transport Complex IV, Evolution, Molecular, Female, Mitochondria, Perciformes, Phylogeny, Sequence Analysis, DNA}, issn = {1095-9513}, doi = {10.1016/j.ympev.2013.09.026}, author = {Taillebois, Laura and Castelin, Magalie and Clara Lord and Chabarria, Ryan and Dettai, Agn{\`e}s and Philippe Keith} } @article {3430, title = {The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e97454}, abstract = {

The scleractinian coral Acropora millepora is one of the most studied species from the Great Barrier Reef. This species has been used to understand evolutionary, immune and developmental processes in cnidarians. It has also been subject of several ecological studies in order to elucidate reef responses to environmental changes such as temperature rise and ocean acidification (OA). In these contexts, several nucleic acid resources were made available. When combined to a recent proteomic analysis of the coral skeletal organic matrix (SOM), they enabled the identification of several skeletal matrix proteins, making A. millepora into an emerging model for biomineralization studies. Here we describe the skeletal microstructure of A. millepora skeleton, together with a functional and biochemical characterization of its occluded SOM that focuses on the protein and saccharidic moieties. The skeletal matrix proteins show a large range of isoelectric points, compositional patterns and signatures. Besides secreted proteins, there are a significant number of proteins with membrane attachment sites such as transmembrane domains and GPI anchors as well as proteins with integrin binding sites. These features show that the skeletal proteins must have strong adhesion properties in order to function in the calcifying space. Moreover this data suggest a molecular connection between the calcifying epithelium and the skeletal tissue during biocalcification. In terms of sugar moieties, the enrichment of the SOM in arabinose is striking, and the monosaccharide composition exhibits the same signature as that of mucus of acroporid corals. Finally, we observe that the interaction of the acetic acid soluble SOM on the morphology of in vitro grown CaCO3 crystals is very pronounced when compared with the calcifying matrices of some mollusks. In light of these results, we wish to commend Acropora millepora as a model for biocalcification studies in scleractinians, from molecular and structural viewpoints.

}, keywords = {Acetic Acid, Amination, Animals, Anthozoa, Bone and Bones, Calcium Carbonate, Crystallization, Gels, Monosaccharides, Proteins, Solubility, Spectroscopy, Fourier Transform Infrared, Spectrum Analysis, Raman}, issn = {1932-6203}, doi = {10.1371/journal.pone.0097454}, author = {Ramos-Silva, Paula and Kaandorp, Jaap and Herbst, Fr{\'e}d{\'e}ric and Plasseraud, Laurent and Alcaraz, G and Stern, Christine and Corneillat, Marion and Guichard, N and Durlet, Christophe and Gilles Luquet and Marin, F} }