• European Marine Science
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Mesopelagic organisms play a critical role in marine ecosystems, channelling energy and organic matter across food webs and serving as the primary prey for many open-ocean predators. Nevertheless, trophic pathways involving mesopelagic organisms are poorly understood and their contribution to food web structure remains difficult to assess (St. John et al., 2016). Existing data to assess mesopelagic feeding interactions and energy transfer are scattered in the literature or remain unpublished, making it difficult to locate and use such datasets. As part of the EU funded project SUMMER - Sustainable Management of Mesopelagic Resources H2020-BG-2018-2, GA: 817806) (https://summerh2020.eu/), we created MesopTroph, a georeferenced database of diet, trophic biogeochemical markers, and energy content of mesopelagic organisms and other marine taxa from the Northeast Atlantic and Mediterranean Sea, compiled from 191 published and non-published sources. MesopTroph includes seven datasets: (i) diet compositions from stomach content analysis, (ii) stable isotopes of carbon and nitrogen (δ13C and δ15N), (iii) fatty acid trophic markers (FATM), (iv) major and trace elements, (v) energy density, (vi) estimates of diet proportions, and (vii) trophic positions. The database contains information from 4918 samples, representing 51119 specimens from 499 species or genera, covering a wide range of trophic guilds and taxonomic groups. Metadata provided for each record include the location, dates and method of sample collection, taxonomic ranks (phylum, class, order, family), number and size (or size range) of sampled organisms, method/model used in data analysis, reference and DOI of the original data source. Compiled data were checked for errors, missing information, and to avoid duplicate entries, and scientific names and taxonomy were standardized.

Short sediment cores were taken at six stations in Wismar Bay, southern Baltic Sea (Germany) in May 2019 using a Rumohr-Lot device. Our aim in this study was to investigate the role of diagenetic element fluxes and different fresh water sources, including submarine groundwater discharge, on the water column in the bay. Porewaters were extracted from the sediment cores by applying the rhizon technique at a resolution between 2 and 5 cm. The porewaters were analyzed for major and trace metals and selected nutrients using a ICP-OES (iCAP, 7400, Duo Thermo Fischer Scientific), total sulphide by a Specord 40 spectrophotometer (Analytik Jena), dissolved inorganic carbon (DIC) and δ13CDIC using an isotope gas mass spectrometre (MAT 253) coupled to a Gasbench II, and δ18OH2O, and δ2HH2O using a CRDS system (laser cavity-ring-down-spectroscopy, Picarro L2140- I). Sediment cores were further sliced at 2 to 4 cm resolution and each freeze-dried solid subsample was analyzed for contents of total carbon, nitrogen, and sulphur using an Elemental Analyzer (Euro Vector EuroEA 3, 052), inorganic carbon using an Elemental Analyzer multi EA (Analytik Jena), total mercury by a DMA-80 analyzer, and HCl-extractable Pb, Mn and Fe using an ICP-OES (iCAP, 7400, Duo Thermo Fischer Scientific).

Abstract Background Nearly 10 years ago, the World Health Organization reported the increasing prevalence of overweight and obesity worldwide as a challenge for public health due to the associated adverse consequences. Epidemiological studies established a firm relationship between an elevated body mass index and chronic conditions such as diabetes, dyslipidemia, hypertension, heart disease, non-alcoholic fatty liver disease, and some types of cancer. Omic studies demonstrated that microRNA (miRNA) profile changes in tissues correlate with a number of diseases, including obesity. Recent studies showed a remarkable stability of miRNAs also in blood, emphasizing their potential as theranostic agents for a variety of disorders and conditions. A number of miRNAs enriched in homeostasis of obesity and metabolic disorders have been characterized in previous researches. Aim This work was finalized to investigate the differential circulating miRNAs signature in early childhood obesity. Our cross-sectional study analyzed the signature of circulating miRNAs in plasma samples of normal weight (n = 159) and overweight/obese (n = 149) children and adolescents participating to the I.Family study, an EC-funded study finalized to investigate the etiology of overweight, obesity and related disorders and the determinants of food choice, lifestyle, and related health outcomes in children and adolescents of eight European countries ( www.ifamilystudy.eu ). Results Differences in miRNA signature with respect to anthropometric and biochemical variables were analyzed. A high degree of variability in levels of circulating miRNAs was identified among children from different countries, in line with recent reports supporting the hypothesis that these molecules are likewise affected by environmental and lifestyle factors. A panel of miRNAs differentially expressed in overweight/low-grade obesity children was characterized (miR-551a and miR-501-5p resulted upregulated; miR-10b-5p, miR-191-3p, miR-215-5p, and miR-874-3p resulted downregulated). ROC curves were also constructed for experimentally confirmed miRNAs. Single miRNAs generally exhibited low AUC values with the highest values for miR-874-3p and miR-501-5p which in combination provided an interesting value (AUC = 0.782). Pearson’s analysis confirmed that miR-10b-5p, miR-215-5p, miR-501-5p, miR-551a, and miR-874-3p significantly correlated with BMI z-score. Molecular interactions of obesity-associated miRNAs were also predicted by bioinformatics tools. Conclusions Our work showed that several circulating miRNAs are differentially represented in overweight/low-grade obesity children and adolescents. Although causal pathways cannot be firmly inferred, it is conceivable that circulating miRNAs may be new biomarkers of early childhood obesity. Trial registration ISRCTN, ISRCTN62310987 . Registered 23/02/2018 - Retrospectively registered.

Abstract Background Arthropod eyes have diversified during evolution to serve multiple needs, such as finding mates, hunting prey and navigating in complex surroundings under varying light conditions. This diversity is reflected in the optical apparatus, photoreceptors and neural circuits that underpin vision. Yet our ability to genetically manipulate the visual system to investigate its function is largely limited to a single species, the fruit fly Drosophila melanogaster. Here, we describe the visual system of Parhyale hawaiensis, an amphipod crustacean for which we have established tailored genetic tools. Results Adult Parhyale have apposition-type compound eyes made up of ~â 50 ommatidia. Each ommatidium contains four photoreceptor cells with large rhabdomeres (R1â 4), expected to be sensitive to the polarisation of light, and one photoreceptor cell with a smaller rhabdomere (R5). The two types of photoreceptors express different opsins, belonging to families with distinct wavelength sensitivities. Using the cis-regulatory regions of opsin genes, we established transgenic reporters expressed in each photoreceptor cell type. Based on these reporters, we show that R1â 4 and R5 photoreceptors extend axons to the first optic lobe neuropil, revealing striking differences compared with the photoreceptor projections found in related crustaceans and insects. Investigating visual function, we show that Parhyale have a positive phototactic response and are capable of adapting their eyes to different levels of light intensity. Conclusions We propose that the visual system of Parhyale serves low-resolution visual tasks, such as orientation and navigation, based on broad gradients of light intensity and polarisation. Optic lobe structure and photoreceptor projections point to significant divergence from the typical organisation found in other malacostracan crustaceans and insects, which could be associated with a shift to low-resolution vision. Our study provides the foundation for research in the visual system of this genetically tractable species.

This dataset contains hydrochemistry and absorption measurements from surface water bodies (standing and flowing water) from Herschel Island, Yukon, Canada collected in 2016 and Cape Bounty Arctic Watershed Observatory, Nunavut, Canada collected in 2017.The detailed methods will be found in the accompanying manuscript. Supplement to: Coch, Caroline; Juhls, Bennet; Lamoureux, Scott F; Lafrenière, Melissa J; Fritz, Michael; Heim, Birgit; Lantuit, Hugues (2019): Comparisons of dissolved organic matter and its optical characteristics in small low and high Arctic catchments. Biogeosciences, Biogeosciences, 16(23), 4535-4553

Abstract Background Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. Results We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. Conclusions We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks.

Astronomical tuning of sediment sequences requires both unambiguous cycle-pattern recognition in climate proxy records and astronomical solutions, and independent information about the phase relationship between these two. Here we present two different astronomically tuned age models for the Oligocene-Miocene Transition (OMT) from Integrated Ocean Drilling Program Site U1334 (equatorial Pacific Ocean) to assess the effect tuning has on astronomically calibrated ages and the geologic time scale. These alternative age models (from ~22 to ~24 Ma) are based on different tunings between proxy records and eccentricity: the first age model is based on an aligning CaCO3 weight (wt%) to Earth's orbital eccentricity, the second age model is based on a direct age calibration of benthic foraminiferal stable carbon isotope ratios (d13C) to eccentricity. To independently test which tuned age model and associated tuning assumptions is in best agreement with independent ages based on tectonic plate-pair spreading rates, we assign our tuned ages to the magnetostratigraphic reversals identified in deep-marine magnetic anomaly profiles. Subsequently, we compute tectonic plate-pair spreading rates based on the tuned ages. The resultant, alternative spreading rate histories indicate that the CaCO3 tuned age model is most consistent with a conservative assumption of constant, or linearly changing, spreading rates. The CaCO3 tuned age model thus provides robust ages and durations for polarity chrons C6Bn.1n-C6Cn.1r, which are not based on astronomical tuning in the latest iteration of the Geologic Time Scale. Furthermore, it provides independent evidence that the relatively large (several 10,000 years) time lags documented in the benthic foraminiferal isotope records relative to orbital eccentricity, constitute a real feature of the Oligocene-Miocene climate system and carbon cycle. The age constraints from Site U1334 thus provide independent evidence that the delayed responses of the Oligocene-Miocene climate-cryosphere system and carbon cycle resulted from highly nonlinear feedbacks to astronomical forcing. Supplement to: Beddow, Helen M; Liebrand, Diederik; Wilson, Douglas S; Hilgen, Frederik J; Sluijs, Appy; Wade, Bridget S; Lourens, Lucas Joost (2018): Astronomical tunings of the Oligocene-Miocene transition from Pacific Ocean Site U1334 and implications for the carbon cycle. Climate of the Past, 14(3), 255-270

Background: The origin of powered avian flight was a locomotor innovation that expanded the ecological potential of maniraptoran dinosaurs, leading to remarkable variation in modern birds (Neornithes). The avian sternum is the anchor for the major flight muscles and, despite varying widely in morphology, has not been extensively studied from evolutionary or functional perspectives. We quantify sternal variation across a broad phylogenetic scope of birds using 3D geometric morphometrics methods. Using this comprehensive dataset, we apply phylogenetically informed regression approaches to test hypotheses of sternum size allometry and the correlation of sternal shape with both size and locomotory capabilities, including flightlessness and the highly varying flight and swimming styles of Neornithes. Results: We find evidence for isometry of sternal size relative to body mass and document significant allometry of sternal shape alongside important correlations with locomotory capability, reflecting the effects of both body shape and musculoskeletal variation. Among these, we show that a large sternum with a deep or cranially projected sternal keel is necessary for powered flight in modern birds, that deeper sternal keels are correlated with slower but stronger flight, robust caudal sternal borders are associated with faster flapping styles, and that narrower sterna are associated with running abilities. Correlations between shape and locomotion are significant but show weak explanatory power, indicating that although sternal shape is broadly associated with locomotory ecology, other unexplored factors are also important. Conclusions: These results display the ecological importance of the avian sternum for flight and locomotion by providing a novel understanding of sternum form and function in Neornithes. Our study lays the groundwork for estimating the locomotory abilities of paravian dinosaurs, the ancestors to Neornithes, by highlighting the importance of this critical element for avian flight, and will be useful for future work on the origin of flight along the dinosaur-bird lineage.