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The N6-methylation of RNA adenosines (N6-methyladenosine, m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq), we generated transcriptome-wide m6A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) exhibiting distinct profiles and being highly methylated compared to transposable element (TE) transcripts. Epitranscriptomes are dynamic and correspond to the chronological steps of development (cleavage, gastrulation, organogenesis, and metamorphosis), with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated with transcript levels, and shifts in methylation profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis, and cell differentiation). The m6A level of TE transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition, and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.

Stéphanie Favrel,1 Anna Urbaniak,2 Izabela Chabowska,3 Anne Sirvent,4 Jean-Philippe Gatignol5 1Innovation Unit, Clinical Department, Pierre Fabre Consumer Health Care, Castres, France; 2Dental Clinic, Gdansk, Poland; 3Dermscan Poland, Gdansk, Poland; 4Eurofins Dermscan, Villeurbanne, France; 5Innovation Unit, Medical Department, Pierre Fabre Consumer Health Care, Castres, FranceCorrespondence: Jean-Philippe GatignolInnovation Unit, Medical Department, Pierre Fabre Consumer Health Care, Péraudel, 17, Avenue Jean Moulin, Castres 81106, FranceTel +33 563 516 804Email jean.philippe.gatignol@pierre-fabre.comPurpose: An innovative hybrid toothbrush was designed to function either in manual sonic mode or combined mode (manual and sonic). The primary objective was to assess the efficacy of a new hybrid powered toothbrush (PTB) used in combined mode versus a comparative manual toothbrush (MTB) for plaque removal, after 14 days of twice-daily use under normal conditions. The secondary objectives were to evaluate the gingival state, to evaluate the tolerance of the hybrid PTB and to evaluate its acceptability.Materials and Methods: This study was a monocentric, block-randomized, dual treatment, parallel group, and examiner-blinded trial with before and after evaluation. It was conducted on two groups of 55 subjects presenting a visible plaque accumulation (score ≥ 2 as measured by the Turesky Modification of the Quigley-Hein Plaque Index (TMQHPI)). On Day 1/Day 8/Day 15, the same investigator conducted blind clinical examinations on each subject and evaluated TMQHPI and Papillary Bleeding Score (PBS). On Day 1, the subjects received either the hybrid PTB or the comparative MTB and used it twice daily under normal conditions of use.Results: The hybrid PTB used in its combined mode eliminates dental plaque more efficiently than the comparative MTB, especially in difficult-to-access areas such as posterior and interproximal dental surfaces, while remaining gentle on the gingivae. The PBS was significantly lower with the hybrid toothbrush compared with the reference manual one.Conclusion: The new device confirmed previous findings and should improve oral hygiene following the manufacturer’s instructions. Moreover, the specific design of the toothbrush means that it can be used according to the oral environment conditions and personal feeling.Keywords: powered toothbrush, sonic toothbrush, dental plaque, oral health

In bilaterian species, the amino acid sequence conservation between Insulin related peptides is relatively low except for the cysteine residues involved in the disulphide bonds. In the A chain, the conserved cystein residues are included in a signature motif. Investigating the variations in this motif would give insight into the phylogenetic history of the family. The table presented in this paper contains a large set of insulin-related peptides in bilateral phylogenetic groups (deuterostomian, ecdysozoan, lophotrochozoan). NCBI databases in silico wide screening combined with bibliographic researches provided a framework for identifying and categorising the structural characteristics of these insulin related peptides. The dataset includes NCBI IDs of each sequence with hyperlinks to FASTA format. Moreover, the structural type (α, β or γ), the A chain motif, the total number of cysteins, the C peptide cleavage mode and the potential additional domains (D or E) are specified for each sequence. The data are associated with the research article “Molecular evolution and functional characterisation of insulin-related peptides in molluscs: contributions of Crassostrea gigas genomic and transcriptomic-wide screening” [1]. The table presented here can be found at http://dx.doi.org/10.17632/w4gr8zcpk5.4#file-21c0f6a5-a3e3-4a15-86e0-e5a696458866.

Les six ONG de conservation de la nature auteures de cet article proposent leur argumentaire pour une évolution de la politique forestière nationale. Celui-ci est fondé suivant cinq grands principes de gestion du bien commun que sont les forêts : 1. Assurer une gestion multifonctionnelle valorisant tous les services écologiques des forêts ; 2. Mettre la biodiversité au coeur de la politique forestière pour faciliter l’adaptation de la gestion ; 3. Accroître l’écoute des attentes de la société, pour mieux y répondre ; 4. Mettre forêts et forestiers en capacité de répondre pleinement aux enjeux inédits de la crise climatique ; 5. Insérer les forêts dans l’aménagement du territoire comme infrastructure verte de l’économie. Ensuite, les six ONG recommandent une orientation politique générale consistant à fonder toute politique forestière sur la charte constitutionnelle de l’environnement de 2004 et proposent 21 mesures structurelles ou opérationnelles.

The neuropeptides involved in the regulation of reproduction in the Pacific oyster (Crassostrea gigas) are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were de novo assembled to generate a specific reference transcriptome of the oyster nervous system and used to identify differentially expressed transcripts. Transcriptome mining led to the identification of novel neuropeptide precursors (NPPs) related to the bilaterian Eclosion Hormone (EH), crustacean female sex hormone/Interleukin 17, Nesfatin, neuroparsin/IGFBP, prokineticins, and urotensin I; to the protostome GNQQN, pleurin, prohormones 3 and 4, prothoracotropic hormones (PTTH), and QSamide/PXXXamide; to the lophotrochozoan CCWamide, CLCCY, HFAamide, and LXRX; and to the mollusk-specific NPPs CCCGS, clionin, FYFY, GNamide, GRWRN, GSWN, GWE, IWMPxxGYxx, LXRYamide, RTLFamide, SLRFamide, and WGAGamide. Among the complete repertoire of NPPs, no sex-biased expression was observed. However, 25 NPPs displayed reproduction stage-specific expression, supporting their involvement in the control of gametogenesis or associated metabolisms.

This paper proposes an original approach to investigate the influence of the geometry of Francis turbines draft tube on pressure fluctuations and energy losses in off-design conditions. It is based on Design of Experiments (DOE) of the draft tube geometry and steady/unsteady Computational Fluid Dynamics (CFD) simulations of the draft tube internal flow. The test case is a Francis turbine unit of specific speed Ns=120 m-kW which is required to operate continuously in off-design conditions, either with 45% (part-load) or 110% (full-load) of the design flow rate. Nine different draft tube geometries featuring a different set of geometrical parameters are first defined by an orthogonal array-based DOE approach. For each of them, unsteady and steady CFD simulations of the internal flow from guide vane to draft tube outlet are performed at part-load and full-load conditions, respectively. The influence of each geometrical parameter on both the flow instability and resulting pressure pulsations, as well as on energy losses in the draft tube, are investigated by applying an Analysis of Means (ANOM) to the numerical results. The whole methodology enables the identification of a set of geometrical parameters minimizing the pressure fluctuations occurring in part-load conditions as well as the energy losses in both full-load and part-load conditions while maintaining the requested pressure recovery. Finally, the results of the CFD simulations with the final draft tube geometry are compared with the results estimated by the ANOM, which demonstrates that the proposed methodology also enables a rough preliminary estimation of the draft tube losses and pressure fluctuations amplitude.

The flow in a Francis turbine at full load is characterised by the development of an axial vortex rope in the draft tube. The vortex rope often promotes cavitation if the turbine is operated at a sufficiently low Thoma number. Furthermore, the vortex rope can evolve from a stable to an unstable behaviour. For CFD, such a flow is a challenge since it requires solving an unsteady cavitating flow including rotor/stator interfaces. Usually, the numerical investigations focus on the cavitation model or the turbulence model. In the present works, attention is paid to the strategy used for the time integration. The vortex rope considered is an unstable cavitating one that develops downstream the runner. The vortex rope shows a periodic behaviour characterized by the development of the vortex rope followed by a strong collapse leading to the shedding of bubbles from the runner area. Three unsteady RANS simulations are performed using the ANSYS CFX 17.2 software. The turbulence and cavitation models are, respectively, the SST and Zwart models. Regarding the time integration, a second order backward scheme is used excepted for the transport equation for the liquid volume fraction, for which a first order backward scheme is used. The simulations differ by the time step and the number of internal loops per time step. One simulation is carried out with a time step equal to one degree of revolution per time step and five internal loops. A second simulation used the same time step but 15 internal loops. The third simulations used three internal loops and an adaptive time step computed based on a maximum CFL lower than 2. The results show an influence of the time integration strategy on the cavitation volume time history both in the runner and in the draft tube with a risk of divergence of the solution if a standard set up is used.

DNA methylation is a critical epigenetic regulator of development in mammals and social insects, but its significance in development outside these groups is not understood. Here we investigated the genome-wide dynamics of DNA methylation in a mollusc model, the oyster Crassostrea gigas, from the egg to the completion of organogenesis. Large-scale methylation maps reveal that the oyster genome displays a succession of methylated and non methylated regions, which persist throughout development. Differentially methylated regions (DMRs) are strongly regulated during cleavage and metamorphosis. The distribution and levels of methylated DNA within genomic features (exons, introns, promoters, repeats and transposons) show different developmental lansdscapes marked by a strong increase in the methylation of exons against introns after metamorphosis. Kinetics of methylation in gene-bodies correlate to their transcription regulation and to distinct functional gene clusters, and DMRs at cleavage and metamorphosis bear the genes functionally related to these steps, respectively. This study shows that DNA methylome dynamics underlie development through transcription regulation in the oyster, a lophotrochozoan species. To our knowledge, this is the first demonstration of such epigenetic regulation outside vertebrates and ecdysozoan models, bringing new insights into the evolution and the epigenetic regulation of developmental processes.

Clémence Guenne,1 Jérôme Fayette,2 Alain Cosmidis,1 Carine Fuchsmann,1 Sophie Tartas,3 Véronique Favrel,4 Philippe Céruse1 1Head and Neck Surgery Department, Lyon-I University, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France; 2Medicine Department, Lyon-I University, Centre Léon Bérard, Lyon, France; 3Medical Oncology Department, Lyon-I University, Hospices Civils de Lyon, Lyon Sud Hospital, 4Radiotherapy Department, Lyon-I University, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France Background: No specific study has focused on patients with metastatic squamous cell carcinoma of the head and neck (SCCHN) at diagnosis. Due to high response rates of induction chemotherapy in chemo-naïve patients with localized disease, their prognosis should be better than patients with recurrent disease.Methods: From January 1, 2008 to July 1, 2012, we retrospectively collected all patients’ records with SCCHN diagnosed as metastatic. Patients, disease, treatment and its results were analyzed. Survival was calculated using the Kaplan–Meier method.Results: Of the 749 new patients treated for SCCHN in our institution, 16 (2.1%) were metastatic at diagnosis, of whom five had cytological results to prove it. Six patients died before treatment or had palliative care and ten received initial chemotherapy and then surgery and/or radiotherapy according to the primary response. Four patients treated with first-line chemotherapy with docetaxel-5FU-cisplatin (TPF) showed a complete response of metastatic lesions allowing locoregional treatment. The overall survival at 1 year and 3 years was 50% and 24%, respectively. The median survival was 7 months (1–72 months). Seven patients (43.7%) had a higher survival at 12 months, including five (31.5%) who are still alive without recurrence with a mean follow-up of 30 months. There was a significant difference in overall survival (P

Triploidy can occur in many animal species but is often lethal. Among invertebrates, amphibians and fishes, triploids are viable although often sterile or infertile. Most triploids of the Pacific oyster Crassostrea gigas are almost sterile (named "3nβ") yet a low but significant proportion show an advanced gametogenesis (named "3nα"). These oysters thus constitute an interesting model to study the effect of triploidy on germ cell development. We used microarrays to compare the gonad transcriptomes of diploid 2n and the abovementioned triploid 3nβ and 3nα male and female oysters throughout gametogenesis.All triploids displayed an upregulation of genes related to DNA repair and apoptosis and a downregulation of genes associated with cell division. The comparison of 3nα and 3nβ transcriptomes with 2n revealed the likely involvement of a cell cycle checkpoint during mitosis in the successful but delayed development of gonads in 3nα individuals. In contrast, a disruption of sex differentiation mechanisms may explain the sterility of 3nβ individuals with 3nβ females expressing male-specific genes and 3nβ males expressing female-specific genes.The disruption of sex differentiation and mitosis may be responsible for the impaired gametogenesis of triploid Pacific oysters. The function of the numerous candidate genes identified in our study should now be studied in detail in order to elucidate their role in sex determination, mitosis/meiosis control, pachytene cell cycle checkpoint, and the control of DNA repair/apoptosis.

BACKGROUND: The Pacific oyster Crassostrea gigas (Mollusca, Lophotrochozoa) is an alternative and irregular protandrous hermaphrodite: most individuals mature first as males and then change sex several times. Little is known about genetic and phenotypic basis of sex differentiation in oysters, and little more about the molecular pathways regulating reproduction. We have recently developed and validated a microarray containing 31,918 oligomers (Dheilly et al., 2011) representing the oyster transcriptome. The application of this microarray to the study of mollusk gametogenesis should provide a better understanding of the key factors involved in sex differentiation and the regulation of oyster reproduction. METHODOLOGY/PRINCIPAL FINDINGS: Gene expression was studied in gonads of oysters cultured over a yearly reproductive cycle. Principal component analysis and hierarchical clustering showed a significant divergence in gene expression patterns of males and females coinciding with the start of gonial mitosis. ANOVA analysis of the data revealed 2,482 genes differentially expressed during the course of males and/or females gametogenesis. The expression of 434 genes could be localized in either germ cells or somatic cells of the gonad by comparing the transcriptome of female gonads to the transcriptome of stripped oocytes and somatic tissues. Analysis of the annotated genes revealed conserved molecular mechanisms between mollusks and mammals: genes involved in chromatin condensation, DNA replication and repair, mitosis and meiosis regulation, transcription, translation and apoptosis were expressed in both male and female gonads. Most interestingly, early expressed male-specific genes included bindin and a dpy-30 homolog and female-specific genes included foxL2, nanos homolog 3, a pancreatic lipase related protein, cd63 and vitellogenin. Further functional analyses are now required in order to investigate their role in sex differentiation in oysters. CONCLUSIONS/SIGNIFICANCE: This study allowed us to identify potential markers of early sex differentiation in the oyster C. gigas, an alternative hermaphrodite mollusk. We also provided new highly valuable information on genes specifically expressed by mature spermatozoids and mature oocytes.

Angiotensin-converting enzyme (ACE) is a highly conserved metallopeptidase. In mammals, the somatic isoform governs blood pressure whereas the germinal isoform (tACE) is required for fertility. In Ecdysozoans, ACE-like enzymes are implicated in reproduction. Despite ACE orthologues being present from bacteria to humans, their function(s) remain(s) unknown in distant organisms such as Lophotrochozoans. In silico analysis of an oyster (Crassostrea gigas) EST library suggested the presence of an ACE orthologue in molluscs. Primer walking and 5'-RACE revealed that the 1.9 kb cDNA encodes CgACE, a 632 amino acid protein displaying a conserved single active site and a putative C-terminal transmembrane anchor, thus resembling human tACE, as supported by molecular modelling. FRET activity assays and Maldi-TOF spectrometry indicated that CgACE is a functional dipeptidyl-carboxypeptidase which is active on Angiotensin I and sensitive to ACE inhibitors and chloride ion concentration. Immunocytochemistry revealed that, as its human counterpart, recombinant CgACE is synthesised as a transmembrane enzyme. RT-qPCR, in-situ hybridization and immunohistochemistry shed light on a tissue, and development stage, specific expression pattern for CgACE, which is increased in the gonad during spermatogenesis. The use of ACE inhibitors in vivo indicates that the dipeptidase activity of CgACE is crucial for the oyster fertilization. Our study demonstrates that a transmembrane active ACE is present in the oyster Crassostrea gigas, and for the first time ascribes a functional role for ACE in Lophotrochozoans. Its biological function in reproduction is conserved from molluscs to humans, a finding of particular evolutionary interest especially since oysters represent the most important aquaculture resource worldwide.

Abstract Background Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations. Results In this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster. Conclusions This study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis.

Abstract Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.