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23,212 Research products, page 1 of 2,322

  • European Marine Science
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  • Open Access
    Authors: 
    DELROISSE, Jérôme; Ullrich-Lüter, Esther; Blaue, Stefanie; Ortega-Martinez, Olga; Eeckhaut, Igor; Flammang, Patrick; Mallefet, Jérôme;
    Publisher: The Royal Society

    Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid Amphiura filiformis. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy Renilla (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the Renilla and Amphiura luciferases allowed us to detect the latter using anti-Renilla luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs in vivo. However, enzymes homologous to the Renilla luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.

  • Open Access
    Authors: 
    Picheral, Marc; Searson, Sarah; Taillandier, V; Bricaud, Annick; Boss, Emmanuel; Stemmann, Lars; Gorsky, G; Tara Oceans Consortium, Coordinators; Tara Oceans Expedition, Participants;
    Publisher: PANGAEA
    Project: TARA | Tara Oceans (2)

    The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set includes properties of seawater, particulate matter and dissolved matter from physical, optical and imaging sensors mounted on a vertical sampling system (Rosette) used during the 2009-2013 tara Oceans Expedition. It comprised 2 pairs of conductivity and temperature sensors (SEABIRD components), and a complete set of WEtLabs optical sensors, including chrorophyll and CDOM fluorometers, a 25 cm transmissiometer, and a one-wavelength backscatter meter. In addition, a SATLANTIC ISUS nitrate sensor and a Hydroptic Underwater Vision Profiler (UVP) were mounted on the rosette. In the Arctic Ocean and Arctic Seas (2013), a second oxygen sensor (SBE43) and a four frequency Aquascat acoustic profiler were added. The system was powered on specific Li-Ion batteries and data were self-recorded at 24HZ. Sensors have all been factory calibrated before, during and after the four year program. Oxygen was validated using climatologies (WOA09). Nitrate and Fluorescence data were adjusted with discrete measurements from Niskin bottles mounted on the Rosette, and optical darks were performed monthly on board. A total of 839 quality checked vertical profiles were made during the tara Oceans expedition 2009-2013.

  • Research data . 2020
    Open Access English
    Authors: 
    Costa, Kassandra M; Hayes, Christopher T; Anderson, Robert F; Pavia, Frank J; Bausch, Alexandra Renee; Deng, Feifei; Dutay, Jean-Claude; Geibert, Walter; Heinze, Christoph; Henderson, Gideon M; +24 more
    Publisher: PANGAEA - Data Publisher for Earth & Environmental Science
    Project: SNSF | SeaO2 - Past changes in S... (144811), ARC | Discovery Projects - Gran... (DP180100048), SNSF | SeaO2 - Past changes in S... (172915)

    In this dataset we present a global compilation of over 1000 sedimentary records of 230Th from across the global ocean at two time slices, the Late Holocene (0-5000 years ago, or 0-5 ka) and the Last Glacial Maximum (18.5-23.5 ka). Data have been screened for age control, errors, and lithogenic corrections. Overall quality levels were computed by summing each record's scores on the individual criteria. A record is optimal if it is based on a chronology that is constrained by δ18O or 14C and it provides both the raw nuclide concentrations and the associated errors. About one quarter of the records in the database achieved this highest quality level. The large majority of the records in the database are good, passing two of the three criteria, while the remaining quarter are of fair or poor quality.

  • Open Access
    Authors: 
    Del Rio, Joaquin; Nogueras Cervera, Marc; Toma, Daniel Mihai; Cadena Muñoz, Javier; Crespin, Júlia; Martinez Padro, Enoc; Carandell Widmer, Matias; Masmitjà Rusiñol, Ivan; Artero Delgado, Carola; Bghiel, Ikram; +7 more
    Publisher: PANGAEA
    Project: EC | JERICO-NEXT (654410), EC | EMSO-Link (731036), EC | EMSODEV (676555), EC | MELOA (776825), EC | NEXOS (614102)
  • Open Access
    Authors: 
    Boulton, Carolyn;
    Publisher: Mendeley
    Project: EC | SEISMIC (335915)

    This text file contains the complete experimental dataset. Data for each experiment listed in Table 1 appear as columns of displacement (mm) and coefficient of friction (mu). Acquired raw torque and normal force data were processed to obtain shear stress and normal stress measurements respectively. The externally measured torque was corrected for fluid pressure and shear displacement-dependent friction of the Teflon-coated O-ring seals using calibration values obtained in runs with a dummy sample of carbon-coated PolyEtherEtherKeton with a known sliding friction; seal friction is typically around 0.03 kN (equivalent to ~1.5 MPa shear stress). The contribution of the Molykote-coated confining rings to the measured friction is negligible (see also den Hartog et al., 2012). The applied normal stress was corrected for the stress supported by the internal seals, the level of which is clearly visible during initial loading and was generally around 0.5 kN (equivalent to ~2 MPa normal stress acting on the sample). Repeat experiments (u644 and u713) on sample 181-1124C-44X-7, 4-6 cm (428.34 mbsf), yielded an analytical error of 0.03-0.05 mu. The analytical error is thought to reflect the fact that the second experiment was performed on the last remaining sample powder, which may have had more fine-grained clays (e.g., sample inter-variability), and/or because of variations in sample preparation.

  • Open Access English
    Authors: 
    Howald, Sarah; Moyano, Marta; Crespel, Amélie; Kuchenmüller, Luis L; Cominassi, Louise; Claireaux, Guy; Peck, Myron A; Mark, Felix Christopher;
    Publisher: PANGAEA - Data Publisher for Earth & Environmental Science

    European sea bass (Dicentrarchus labrax) is a large, economically important fish species with a long generation time whose long-term resilience to ocean acidification (OA) and warming (OW) is not clear. We incubated sea bass from Brittany (France) for two generations (>5 years in total) under ambient and predicted OA conditions (PCO2: 650 and 1700 µatm) crossed with ambient and predicted ocean OW conditions in F1 (temperature: 15-18°C and 20-23°C) to investigate the effects of climate change on larval and juvenile growth and metabolic rate.We found that in F1, OA as single stressor at ambient temperature did not affect larval or juvenile growth and OW increased developmental time and growth rates, but OAW decreased larval size at metamorphosis. Larval routine and juvenile standard metabolic rates were significantly lower in cold compared to warm conditioned fish and also lower in F0 compared to F1 fish. We did not find any effect of OA as a single stressor on metabolic rates. Juvenile PO2crit was not affected by OA or OAW in both generations.We discuss the potential underlying mechanisms resulting in the resilience of F0 and F1 larvae and juveniles to OA and in the beneficial effects of OW on F1 larval growth and metabolic rate, but on the other hand in the vulnerability of F1, but not F0 larvae to OAW. With regard to the ecological perspective, we conclude that recruitment of larvae and early juveniles to nursery areas might decrease under OAW conditions but individuals reaching juvenile phase might benefit from increased performance at higher temperatures. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2022-06-29.

  • Open Access
    Authors: 
    L. Chouinard-Thuly; A. R. Reddon; I. Leris; R. L. Earley; S. M. Reader;
    Publisher: The Royal Society
    Project: NSERC

    Read me file containing the information about the data presented in the data set document.

  • Open Access
    Authors: 
    Wang, Rong-Lin; Biales, Adam; Garcia-Reyero, Natalia; Perkins, Edward; Villeneuve, Daniel; Ankley, Gerald; Bencic, David;
    Publisher: Figshare

    A complete list of microarray data used in the current study. (XLSX 111Â kb)

  • Open Access
    Authors: 
    Seear, Paul J; Tarling, Geraint A; Burns, Gavin; Goodall-Copestake, William P; Gaten, Edward; Özkaya, Özge; Rosato, Ezio;
    Publisher: figshare

    Additional file 1: All transcripts differentially expressed more than twofold (p < 0.05) relative to C early in each moult cluster group. Each sheet in the file lists transcripts that were differentially expressed more than twofold (B&H adjusted p < 0.05) relative to C early for each moult cluster group. Each transcript is listed with GenBank accession number, contig/singleton identifier, top BLAST (E < 1e-5) description (tBLASTX hits are underlined, all others are BLASTX), E value of the BLAST hit, Gene Ontology identifiers (C = cellular component, F = molecular function, P = biological process), Pfam protein domain (E < 1e-5), fold change (with inverted fold change for down regulated transcripts) and false discovery rate adjusted p value. (XLS 272 KB)

  • Open Access
    Authors: 
    Carrier, Tyler J.; Maldonado, Manuel; Schmittmann, Lara; Pita, Lucía; Bosch, Thomas C. G.; Hentschel, Ute;
    Publisher: figshare

    Additional file 1: Table S1. Sponge species with known relations to microorganisms during development and corresponding characteristics. Table S2. Sponge developmental stages microbiome sampled used in meta-analysis. Table S3. Alpha diversity measures for each sponge developmental stages. Table S4. Relative abundance of bacterial phyla for all species of sponge developmental stages. Table S5. Summary of statistical tests for alpha diversity between HMA and LMA sponges. Table S6. Sponge species with profiled bacterial communities and known as an LMA or HMA. Table S7. Summary of PERMANOVA results for compositional comparisons between sponge species and symbiont life-style. Table S8. GenBank accession numbers for 18S rRNS sequences used in gene tree as part of phylosymbiosis. Table S9. Statistical tables for testing phylosymbiosis across geminate species pairs. Table S10. Average alpha rarefaction values for each species based on observed ASVs and phylogenetic diversity [232–267].

Advanced search in Research products
Research products
arrow_drop_down
Searching FieldsTerms
Any field
arrow_drop_down
includes
arrow_drop_down
Include:
The following results are related to European Marine Science. Are you interested to view more results? Visit OpenAIRE - Explore.
23,212 Research products, page 1 of 2,322
  • Open Access
    Authors: 
    DELROISSE, Jérôme; Ullrich-Lüter, Esther; Blaue, Stefanie; Ortega-Martinez, Olga; Eeckhaut, Igor; Flammang, Patrick; Mallefet, Jérôme;
    Publisher: The Royal Society

    Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid Amphiura filiformis. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy Renilla (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the Renilla and Amphiura luciferases allowed us to detect the latter using anti-Renilla luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs in vivo. However, enzymes homologous to the Renilla luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.

  • Open Access
    Authors: 
    Picheral, Marc; Searson, Sarah; Taillandier, V; Bricaud, Annick; Boss, Emmanuel; Stemmann, Lars; Gorsky, G; Tara Oceans Consortium, Coordinators; Tara Oceans Expedition, Participants;
    Publisher: PANGAEA
    Project: TARA | Tara Oceans (2)

    The Tara Oceans Expedition (2009-2013) sampled the world oceans on board a 36 m long schooner, collecting environmental data and organisms from viruses to planktonic metazoans for later analyses using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set includes properties of seawater, particulate matter and dissolved matter from physical, optical and imaging sensors mounted on a vertical sampling system (Rosette) used during the 2009-2013 tara Oceans Expedition. It comprised 2 pairs of conductivity and temperature sensors (SEABIRD components), and a complete set of WEtLabs optical sensors, including chrorophyll and CDOM fluorometers, a 25 cm transmissiometer, and a one-wavelength backscatter meter. In addition, a SATLANTIC ISUS nitrate sensor and a Hydroptic Underwater Vision Profiler (UVP) were mounted on the rosette. In the Arctic Ocean and Arctic Seas (2013), a second oxygen sensor (SBE43) and a four frequency Aquascat acoustic profiler were added. The system was powered on specific Li-Ion batteries and data were self-recorded at 24HZ. Sensors have all been factory calibrated before, during and after the four year program. Oxygen was validated using climatologies (WOA09). Nitrate and Fluorescence data were adjusted with discrete measurements from Niskin bottles mounted on the Rosette, and optical darks were performed monthly on board. A total of 839 quality checked vertical profiles were made during the tara Oceans expedition 2009-2013.

  • Research data . 2020
    Open Access English
    Authors: 
    Costa, Kassandra M; Hayes, Christopher T; Anderson, Robert F; Pavia, Frank J; Bausch, Alexandra Renee; Deng, Feifei; Dutay, Jean-Claude; Geibert, Walter; Heinze, Christoph; Henderson, Gideon M; +24 more
    Publisher: PANGAEA - Data Publisher for Earth & Environmental Science
    Project: SNSF | SeaO2 - Past changes in S... (144811), ARC | Discovery Projects - Gran... (DP180100048), SNSF | SeaO2 - Past changes in S... (172915)

    In this dataset we present a global compilation of over 1000 sedimentary records of 230Th from across the global ocean at two time slices, the Late Holocene (0-5000 years ago, or 0-5 ka) and the Last Glacial Maximum (18.5-23.5 ka). Data have been screened for age control, errors, and lithogenic corrections. Overall quality levels were computed by summing each record's scores on the individual criteria. A record is optimal if it is based on a chronology that is constrained by δ18O or 14C and it provides both the raw nuclide concentrations and the associated errors. About one quarter of the records in the database achieved this highest quality level. The large majority of the records in the database are good, passing two of the three criteria, while the remaining quarter are of fair or poor quality.

  • Open Access
    Authors: 
    Del Rio, Joaquin; Nogueras Cervera, Marc; Toma, Daniel Mihai; Cadena Muñoz, Javier; Crespin, Júlia; Martinez Padro, Enoc; Carandell Widmer, Matias; Masmitjà Rusiñol, Ivan; Artero Delgado, Carola; Bghiel, Ikram; +7 more
    Publisher: PANGAEA
    Project: EC | JERICO-NEXT (654410), EC | EMSO-Link (731036), EC | EMSODEV (676555), EC | MELOA (776825), EC | NEXOS (614102)
  • Open Access
    Authors: 
    Boulton, Carolyn;
    Publisher: Mendeley
    Project: EC | SEISMIC (335915)

    This text file contains the complete experimental dataset. Data for each experiment listed in Table 1 appear as columns of displacement (mm) and coefficient of friction (mu). Acquired raw torque and normal force data were processed to obtain shear stress and normal stress measurements respectively. The externally measured torque was corrected for fluid pressure and shear displacement-dependent friction of the Teflon-coated O-ring seals using calibration values obtained in runs with a dummy sample of carbon-coated PolyEtherEtherKeton with a known sliding friction; seal friction is typically around 0.03 kN (equivalent to ~1.5 MPa shear stress). The contribution of the Molykote-coated confining rings to the measured friction is negligible (see also den Hartog et al., 2012). The applied normal stress was corrected for the stress supported by the internal seals, the level of which is clearly visible during initial loading and was generally around 0.5 kN (equivalent to ~2 MPa normal stress acting on the sample). Repeat experiments (u644 and u713) on sample 181-1124C-44X-7, 4-6 cm (428.34 mbsf), yielded an analytical error of 0.03-0.05 mu. The analytical error is thought to reflect the fact that the second experiment was performed on the last remaining sample powder, which may have had more fine-grained clays (e.g., sample inter-variability), and/or because of variations in sample preparation.

  • Open Access English
    Authors: 
    Howald, Sarah; Moyano, Marta; Crespel, Amélie; Kuchenmüller, Luis L; Cominassi, Louise; Claireaux, Guy; Peck, Myron A; Mark, Felix Christopher;
    Publisher: PANGAEA - Data Publisher for Earth & Environmental Science

    European sea bass (Dicentrarchus labrax) is a large, economically important fish species with a long generation time whose long-term resilience to ocean acidification (OA) and warming (OW) is not clear. We incubated sea bass from Brittany (France) for two generations (>5 years in total) under ambient and predicted OA conditions (PCO2: 650 and 1700 µatm) crossed with ambient and predicted ocean OW conditions in F1 (temperature: 15-18°C and 20-23°C) to investigate the effects of climate change on larval and juvenile growth and metabolic rate.We found that in F1, OA as single stressor at ambient temperature did not affect larval or juvenile growth and OW increased developmental time and growth rates, but OAW decreased larval size at metamorphosis. Larval routine and juvenile standard metabolic rates were significantly lower in cold compared to warm conditioned fish and also lower in F0 compared to F1 fish. We did not find any effect of OA as a single stressor on metabolic rates. Juvenile PO2crit was not affected by OA or OAW in both generations.We discuss the potential underlying mechanisms resulting in the resilience of F0 and F1 larvae and juveniles to OA and in the beneficial effects of OW on F1 larval growth and metabolic rate, but on the other hand in the vulnerability of F1, but not F0 larvae to OAW. With regard to the ecological perspective, we conclude that recruitment of larvae and early juveniles to nursery areas might decrease under OAW conditions but individuals reaching juvenile phase might benefit from increased performance at higher temperatures. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2021) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2022-06-29.

  • Open Access
    Authors: 
    L. Chouinard-Thuly; A. R. Reddon; I. Leris; R. L. Earley; S. M. Reader;
    Publisher: The Royal Society
    Project: NSERC

    Read me file containing the information about the data presented in the data set document.

  • Open Access
    Authors: 
    Wang, Rong-Lin; Biales, Adam; Garcia-Reyero, Natalia; Perkins, Edward; Villeneuve, Daniel; Ankley, Gerald; Bencic, David;
    Publisher: Figshare

    A complete list of microarray data used in the current study. (XLSX 111Â kb)

  • Open Access
    Authors: 
    Seear, Paul J; Tarling, Geraint A; Burns, Gavin; Goodall-Copestake, William P; Gaten, Edward; Özkaya, Özge; Rosato, Ezio;
    Publisher: figshare

    Additional file 1: All transcripts differentially expressed more than twofold (p < 0.05) relative to C early in each moult cluster group. Each sheet in the file lists transcripts that were differentially expressed more than twofold (B&H adjusted p < 0.05) relative to C early for each moult cluster group. Each transcript is listed with GenBank accession number, contig/singleton identifier, top BLAST (E < 1e-5) description (tBLASTX hits are underlined, all others are BLASTX), E value of the BLAST hit, Gene Ontology identifiers (C = cellular component, F = molecular function, P = biological process), Pfam protein domain (E < 1e-5), fold change (with inverted fold change for down regulated transcripts) and false discovery rate adjusted p value. (XLS 272 KB)

  • Open Access
    Authors: 
    Carrier, Tyler J.; Maldonado, Manuel; Schmittmann, Lara; Pita, Lucía; Bosch, Thomas C. G.; Hentschel, Ute;
    Publisher: figshare

    Additional file 1: Table S1. Sponge species with known relations to microorganisms during development and corresponding characteristics. Table S2. Sponge developmental stages microbiome sampled used in meta-analysis. Table S3. Alpha diversity measures for each sponge developmental stages. Table S4. Relative abundance of bacterial phyla for all species of sponge developmental stages. Table S5. Summary of statistical tests for alpha diversity between HMA and LMA sponges. Table S6. Sponge species with profiled bacterial communities and known as an LMA or HMA. Table S7. Summary of PERMANOVA results for compositional comparisons between sponge species and symbiont life-style. Table S8. GenBank accession numbers for 18S rRNS sequences used in gene tree as part of phylosymbiosis. Table S9. Statistical tables for testing phylosymbiosis across geminate species pairs. Table S10. Average alpha rarefaction values for each species based on observed ASVs and phylogenetic diversity [232–267].