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  • European Marine Science
  • 2017-2021
  • Open Access
  • Publications
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  • European Commission
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  • ZENODO

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Troupin, Charles; Barth, Alexander;

    Report presenting the results of the spatial interpolation of radial velocity from high-frequency radar systems in Europe. The tool for the interpolation is DIVAnd and in particular its version for the interpolation of velocity (DIVAnd_HFRadar.jl)

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    ZENODO
    Report . 2022
    License: CC BY
    Data sources: Datacite
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    ZENODO
    Report . 2022
    License: CC BY
    Data sources: ZENODO
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    ZENODO
    Report . 2021
    License: CC BY
    Data sources: ZENODO
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      ZENODO
      Report . 2022
      License: CC BY
      Data sources: Datacite
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      ZENODO
      Report . 2022
      License: CC BY
      Data sources: ZENODO
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      ZENODO
      Report . 2021
      License: CC BY
      Data sources: ZENODO
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Potrich, Davide; Zanon, Mirko; Vallortigara, Giorgio;

    Debates have arisen as to whether non-human animals actually can learn abstract non-symbolic numerousness or whether they always rely on some continuous physical aspect of the stimuli, covarying with number. Here we investigated archerfish (Toxotes jaculatrix) non-symbolic numerical discrimination with accurate control for co-varying continuous physical stimulus attributes. Archerfish were trained to select one of two groups of black dots (Exp. 1: 3 vs. 6 elements; Exp. 2: 2 vs. 3 elements); these were controlled for several combinations of physical variables (elements' size, overall area, overall perimeter, density and sparsity), ensuring that only numerical information was available. Generalization tests with novel numerical comparisons (2 vs. 3, 5 vs. 8 and 6 vs. 9 in Exp. 1; 3 vs. 4, 3 vs. 6 in Exp. 2) revealed choice for the largest or smallest numerical group according to the relative number that was rewarded at training. None of the continuous physical variables, including spatial frequency, were affecting archerfish performance. Results provide evidence that archerfish spontaneously use abstract relative numerical information for both small and large numbers when only numerical cues are available.

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    DRYAD; ZENODO
    Dataset . 2021 . 2022
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      Dataset . 2021 . 2022
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    Authors: Xavier, Joao; Pinto, Francisc; Wang, Zhe; Rhee, Kyu; +3 Authors

    Metabolomic data preprocessing. The extracts were profiled using liquid-chromatography coupled to mass spectrometry (LC-MS), identifying a total of 92 compounds (Supplementary Fig. 5). Some compounds contained missing values. These missing values in metabolite abundance can be (1) truly missing; (2) present in a sample but its level is below detection limit; (3) present in a sample at a level above the detection limit but missing due to failure of algorithms in data processing. Here we assume that a metabolite with missing values in all three replicates is truly missing in the sample and removed from our analysis (Supplementary Fig. 5). However, if the missing values were only found in one or two replicates, the missing values were imputed by the average of the non-missing values. After that imputation all compounds with missing values were removed (Supplementary Fig. 5). The peak areas were normalized using Cross-Contribution Compensating Multiple Standard Normalization (CCMN) (80) with NormalizeMets R package (81). This method relies on the use of multiple internal standards. Since LC-MS lacks such internal standards, we used instead a set of metabolites assumed to be constant across all the strains. They were selected with a Kuskal-Wallis test, adjusting the p-value with Benjamini-Hochberg method. The ones with a p-value above 0.05 were considered constant (pyruvate, methylglyoxal, (S)-2-Acetolactate, Tyramine, D-Glucose, (S)-Lactate, N-acetyl-L-glutamate 5-semialdehyde, 4-Aminobutyraldehyde and Glycine), therefore after the normalization step they were removed (indicated in red, Supplementary Fig. 5A). The processed area peaks for all metabolites are included in Supplementary Table 5. Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large groups and cooperatively secrete massive amounts of secondary metabolites that impact their environment. Yet, the conditions enabling secondary metabolism without compromising primary needs remain unclear. Here we investigated the biosynthesis of thamnolipids, a secondary metabolite that Pseudomonas aeruginosa makes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that biosynthesis of rhamnolipids from glycerol varies inconsistently across the phylogenetic tree; instead, non-producer lineages are also those worse at reducing the oxidative stress of primary glycerol metabolism. The link to oxidative stress explains the inconsistent distribution across the P. aeruginosa tree, adding a new layer to the regulation of rhamnolipids—a microbial secondary metabolite important for fitness in natural and clinical settings. Metabolite extraction. All P. aeruginosa strains were grown until the end of exponential phase of growth in glycerol minimal medium. Bacteria was then loaded into 0.25 μm nylon membranes (Millipore) using vacuum, transferred to pre-warmed hard agar plates with the same medium composition and incubated at 37ºC during 2.5 h. The filters were then passed to 35 mm polystyrene dishes (Falcon) with 1 mL of 2:2:1 methanol:acetonitrile:H2O quenching buffer and incubated there during 15 minutes on dry ice. Cells were removed by scraping and the lysate containing quenching buffer was transferred to 1.5 mL tubes and centrifuged at 16000 rpm for 10 minutes at 4ºC. Supernatant transferred to fresh tubes and stored at -80ºC.

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    DRYAD; ZENODO
    Dataset . 2021
    License: CC 0
    Data sources: Datacite; ZENODO
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      DRYAD; ZENODO
      Dataset . 2021
      License: CC 0
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Athanasios Gkanasos; Kostas Tsiaras; George Triantaphyllidis; Aleksandros Panagopoulos; +7 Authors

    Marine pollution from debris is a major issue nowadays, since every year large amounts of litter enter into the sea. Under the Horizon 2020 framework and within the Cleaning Litter by developing and Applying Innovative Methods in European Seas (CLAIM) project, innovative devices were designed, developed, tested and applied in laboratory and in the field. These consisted of a system named CLEAN TRASH for the prevention of macrolitter in river estuaries before entering the Sea and a filtering system for microplastics (MPs), to be placed at waste water treatment plants (WWTP). Laboratory experiments showed that macrolitters were blocked by 90% by the CLEAN TRASH system, while during the sea testing period at the Kifissos river estuary, a significant source of terrestrial based litter for the Saronikos Gulf, a total amount of 1,175 kg of litter was collected in 38 days before entering the sea, of which the 708 kg (60%) were plastic debris of various sizes and another 164 kg (14%) of styrofoam parts. The lab scale prototype of the filtering system for MPs had an efficiency of about 95%. The upscaled device was tested at the Megara WWTP and was able to withhold a significant amount of MPs. The theoretical contribution of such devices toward the reduction of plastic pollution in the Saronikos Gulf area and the Natura conservation areas therein, was also studied with the use of a 3-D coupled Hydrodynamic-Lagrangian litter tracking model. In all experiments performed, the installation of the above devices for a period of 2 years, resulted in a microplastics reduction by about 87% and a macroplastics reduction ranging from 13 to 43%, depending on the sources.

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    Frontiers in Marine Science
    Article
    License: CC BY
    Data sources: UnpayWall
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    DOAJ
    Article . 2021
    Data sources: DOAJ
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      Frontiers in Marine Science
      Article
      License: CC BY
      Data sources: UnpayWall
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      DOAJ
      Article . 2021
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Garcia-Souto, Daniel; Diaz-Costas, Seila; Bruzos, Alicia L; Rocha, Sara; +14 Authors

    We performed whole-genome sequencing on 23 samples from 16 clam specimens, which includes eight neoplastic and eight non-neoplastic animals (Table 1), with Illumina paired-end libraries of 350 bp insert size and reads 150 bp long. Then, we run MITObim v1.9.1 (Hahn, et al. 2013) to assemble the full mitochondrial genome of all sequenced samples, using gene baits from the following Cox1 and 16S reference genes to prime the assembly of clam mitochondrial genomes: V. verrucosa (Cox1, with GenBank accession number KC429139, 16S: C429301), C. gallina (Cox1: KY547757, 16S: KY547777) and C. striatula (Cox1: KY547747, 16S: KY547767). The draft sequences were polished twice with Pilon v1.23 (Walker, et al. 2014), and conflictive repetitive fragments from the mitochondrial control region were resolved using long read sequencing with Oxford Nanopore technologies (ONT) on a set of representative samples from each species and tumours. ONT reads were assembled with Miniasm v0.3 (Li 2016) and corrected using Racon v1.3.1 (Vaser, et al. 2017). Protein-coding genes, rDNAs and tRNAs were annotated on the curated mitochondrial genomes using MITOS2 web server (Bernt, et al. 2013), and manually curated to fit ORFs as predicted by ORF-FINDER (Rombel, et al. 2002). The rebuilt sequences can be found here in VVE_CGA_Mitochondrial_DNA.fasta and the annotations in VVE_CGA_Mitochondrial_DNA.gff. We then mapped the paired-end sequencing data from healthy and neoplastic tissues from all neoplastic samples onto the V. verrucosa and C. gallina reference mitochondrial genomes using BWA-mem v0.7.17-r1188 (Li and Durbin 2009) with default parameters. Duplicate reads were marked with Picard 2.18.14 and removed from the analysis. The employed reference genome can be found in Ref_CGA_VVE.fa, and each bam file corresponds to a given animal (i.e. PLVV18_2249F-N0-alnCGA_VVE.sorted.detup.bam) in which the code represents the country (P, Portugal), and the locality (L, Lisbon) of procedence, the species (VV, Venus verrucosa), the year of collection (18, 2018), an internal code of the animal (2249) and the sequenced tissue (F, Foot; Also H from Haemolymph and G from Gill). Some of them were obtained from Whole genome amplified samples (WGA). There is a reference to the intensity of the neoplasia detected in the animal (N0=Healthy; N1, N2, N3 = different levels of neoplasia; N? = neoplasia but level unknown). COI Veneridae sequences were recovered from Genbank and Boldsystems and aligned with our mitochondria reconstructions and are in the COX_all_Venerids.phy file. This was later employed to reconstruct a molecular ML phylogeny shown as supplementary data in our manuscript. DEAH12 and TFIIH sequences, alignments and molecular phylogenies can be found here as well (alignments and trees). Satellite monomer clusters CL04 and CL17 reconstructions as recovered from repeatexplorer (Novak et al. 2010) from C. gallina NGS data can be found at "Satellite_references.fasta" and coverage stats for each of the specimens with NGS data here is present in Satellite_coverage.txt. Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukemia-like transmissible cancers, called hemic neoplasias, have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight V. verrucosa clams that were diagnosed with hemic neoplasia, from two sampling points located more than 1,000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing of tumour tissues from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukemia originated in C. gallina (or a closely related taxa) and was later transmitted to V. verrucosa, in which it survived as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all the studied tumours belonging to a single neoplastic C. gallina lineage that spread in the Seas of Southern Europe.

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    DRYAD; ZENODO
    Dataset . 2021
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      DRYAD; ZENODO
      Dataset . 2021
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    Authors: Sandven, Stein; Higgins, Ruth;

    This booklet provides a summary of the scientific research carried out on the INTAROS project from 2016-2021, towards an Integrated Arctic Observing System

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    Authors: Royston, Sam; Brady, Aoibheann; Chuter, Stephen J; Vishwakarma, Bramha D; +3 Authors

    eLightning presentation at AGU Fall Meeting 2021, online, 13-17 December 2021, New Orleans

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    Authors: O'Donncha, Fearghal; Akhriev, Albert; Eck, Bradley; Burke, Meredith; +2 Authors

    Machine learning has not achieved the same degree of success in environmental applications as in other industries. Challenges around data sparsity, quality, and consistency have limited the impact of deep neural network approaches and restricted the focus to research applications. An alternative approach -- that is more amenable to the characteristics of data coming from disparate IoT devices deployed at different times and locations in the ocean -- is to develop many lightweight models that can be readily scaled up or down based on the number of devices available at any time. This paper presents a serverless framework that naturally marries a single IoT sensor device with a forecasting model. Aspects related to data ingestion, data processing, model training and deployment are described. The framework is applied to a fish farm site in Atlantic Canada.

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    Authors: Koch, Marcus; Wolf, Eva;

    The data supplements contain: a) Supplementary Data Set 1 SupplementaryDataSet1_CytogeneticDataSurvey.xlsx This file contains 575 georeferenced chromosome counts and/or genome sizes across the Cochlearia genus. b) Supplementary Data Set 2 SupplementaryDataSet2_AccessionDetailsNGSdata.xlsx This file contains detailed information on 65 Cochlearia samples and 3 Ionopsidium samples included in NGS data generation and analysis. c) Supplementary Data Set 3 SupplementaryDataSet3_MetabolicCompoundMatrix.xlsx This file contains raw and normalized tables of 40 metabolic compounds consistently detected in all analyzed samples. d) Supplementary Data Set 4 SupplementaryDataSet4_FlowCytometrySummaryTable.xlsx This file contains detailed flow cytometry results. d) Supplementary Data Set 5 SupplementaryDataSet5_PlastomeAlignment.txt This file provides the plastome alignment as used for RAxML and BEAST analyses. e) Supplementary Data Set 6 SupplementaryDataSet6_PlastomePartitionfileRaxmlBEAST.txt This file contains data partitioning schemes for plastome RAxML and BEAST analyses. f) Supplementary Data Set 7 SupplementaryDataSet7_MitochondrialContigs.zip This folder contains annotated mitochondrial de novo consensus sequences of sample Cmica_0979 (in Genbank Flat File Format (*.gb)), as used as reference sequences in reference-based mappings and named as follows: SupplementaryDataSet7a.gb SupplementaryDataSet7b.gb SupplementaryDataSet7c.gb SupplementaryDataSet7d.gb SupplementaryDataSet7e.gb SupplementaryDataSet7f.gb SupplementaryDataSet7g.gb SupplementaryDataSet7h.gb g) Supplementary Data Set 8 SupplementaryDataSet8_MitochondrialGenomeAlignment.txt This file provides the alignment of mitochondrial genome sequences as inputted into RAxML analysis. h) Supplementary Data Set 9 SupplementaryDataSet9_nrSNPalignmentRAxML.phy This file provides the alignment of transcriptome-wide nuclear SNPs in phylip format as inputted into RAxML analysis. i) Supplementary Data Set 10 SupplementaryDataSet10_nrSNPsSplitstreeTreemix.vcf.zip This file provides hard-filtered biallelic transcriptome-wide nuclear SNPs in VCF format as used for SplitsTree and TreeMix analyses. j) Supplementary Data Set 11 SupplementaryDataSet11_nrSNPsStructure.txt This file provides the input for the STRUCTURE analysis of 62 Cochlearia samples. k) Supplementary Data Set 12 SupplementaryDataSet12_nrSNPsStructureBavarica.txt This file provides the input for the STRUCTURE analysis of Cochlearia bavarica. l) Supplementary Data Set 13 SupplementaryDataSet13_nrSNPsABC.vcf.gz This file provides the input for the ABC modelling in VCF format. With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This sudden change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed central carbon metabolism responses to cold in diverse species and ecotypes, likely due to continuous connections to cold habitats that may have facilitated widespread adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.

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    Authors: Jean-Baptiste Sallée; Violaine Pellichero; Camille Akhoudas; Etienne Pauthenet; +5 Authors

    This object includes two files. One (GlobalML_Trend_1970_2018.mat) contains the 1970-2018 trends of mixed-layer depth, 0-200 stratification, and pycnocline stratification, as described in: Sallée, J.B., Pellichero, V., Akhoudas, C., Pauthenet, E., Vignes, L., Schmidtko, S., Naveira Garabato, A., Sutherland, P., Kuusela, M., 2020, Fifty-year changes of the world ocean’s surface layer in response to climate change, 591, 592–598, https://doi.org/10.1038/s41586-021-03303-x. The second one (GlobalML_Climato_1970_2018.mat) contains a climatology of mixed-layer depth based on the same methodology as in Sallée et al., 2021 (nature; doi:https://doi.org/10.1038/s41586-021-03303-x) but without regressing a trend. The climatological field is therefore different than in the paper; more robust in region where trends are unphysical (e.g. winter high latitude)

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    Authors: Troupin, Charles; Barth, Alexander;

    Report presenting the results of the spatial interpolation of radial velocity from high-frequency radar systems in Europe. The tool for the interpolation is DIVAnd and in particular its version for the interpolation of velocity (DIVAnd_HFRadar.jl)

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    Authors: Potrich, Davide; Zanon, Mirko; Vallortigara, Giorgio;

    Debates have arisen as to whether non-human animals actually can learn abstract non-symbolic numerousness or whether they always rely on some continuous physical aspect of the stimuli, covarying with number. Here we investigated archerfish (Toxotes jaculatrix) non-symbolic numerical discrimination with accurate control for co-varying continuous physical stimulus attributes. Archerfish were trained to select one of two groups of black dots (Exp. 1: 3 vs. 6 elements; Exp. 2: 2 vs. 3 elements); these were controlled for several combinations of physical variables (elements' size, overall area, overall perimeter, density and sparsity), ensuring that only numerical information was available. Generalization tests with novel numerical comparisons (2 vs. 3, 5 vs. 8 and 6 vs. 9 in Exp. 1; 3 vs. 4, 3 vs. 6 in Exp. 2) revealed choice for the largest or smallest numerical group according to the relative number that was rewarded at training. None of the continuous physical variables, including spatial frequency, were affecting archerfish performance. Results provide evidence that archerfish spontaneously use abstract relative numerical information for both small and large numbers when only numerical cues are available.

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    Authors: Xavier, Joao; Pinto, Francisc; Wang, Zhe; Rhee, Kyu; +3 Authors

    Metabolomic data preprocessing. The extracts were profiled using liquid-chromatography coupled to mass spectrometry (LC-MS), identifying a total of 92 compounds (Supplementary Fig. 5). Some compounds contained missing values. These missing values in metabolite abundance can be (1) truly missing; (2) present in a sample but its level is below detection limit; (3) present in a sample at a level above the detection limit but missing due to failure of algorithms in data processing. Here we assume that a metabolite with missing values in all three replicates is truly missing in the sample and removed from our analysis (Supplementary Fig. 5). However, if the missing values were only found in one or two replicates, the missing values were imputed by the average of the non-missing values. After that imputation all compounds with missing values were removed (Supplementary Fig. 5). The peak areas were normalized using Cross-Contribution Compensating Multiple Standard Normalization (CCMN) (80) with NormalizeMets R package (81). This method relies on the use of multiple internal standards. Since LC-MS lacks such internal standards, we used instead a set of metabolites assumed to be constant across all the strains. They were selected with a Kuskal-Wallis test, adjusting the p-value with Benjamini-Hochberg method. The ones with a p-value above 0.05 were considered constant (pyruvate, methylglyoxal, (S)-2-Acetolactate, Tyramine, D-Glucose, (S)-Lactate, N-acetyl-L-glutamate 5-semialdehyde, 4-Aminobutyraldehyde and Glycine), therefore after the normalization step they were removed (indicated in red, Supplementary Fig. 5A). The processed area peaks for all metabolites are included in Supplementary Table 5. Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large groups and cooperatively secrete massive amounts of secondary metabolites that impact their environment. Yet, the conditions enabling secondary metabolism without compromising primary needs remain unclear. Here we investigated the biosynthesis of thamnolipids, a secondary metabolite that Pseudomonas aeruginosa makes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that biosynthesis of rhamnolipids from glycerol varies inconsistently across the phylogenetic tree; instead, non-producer lineages are also those worse at reducing the oxidative stress of primary glycerol metabolism. The link to oxidative stress explains the inconsistent distribution across the P. aeruginosa tree, adding a new layer to the regulation of rhamnolipids—a microbial secondary metabolite important for fitness in natural and clinical settings. Metabolite extraction. All P. aeruginosa strains were grown until the end of exponential phase of growth in glycerol minimal medium. Bacteria was then loaded into 0.25 μm nylon membranes (Millipore) using vacuum, transferred to pre-warmed hard agar plates with the same medium composition and incubated at 37ºC during 2.5 h. The filters were then passed to 35 mm polystyrene dishes (Falcon) with 1 mL of 2:2:1 methanol:acetonitrile:H2O quenching buffer and incubated there during 15 minutes on dry ice. Cells were removed by scraping and the lysate containing quenching buffer was transferred to 1.5 mL tubes and centrifuged at 16000 rpm for 10 minutes at 4ºC. Supernatant transferred to fresh tubes and stored at -80ºC.

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    DRYAD; ZENODO
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    Authors: Athanasios Gkanasos; Kostas Tsiaras; George Triantaphyllidis; Aleksandros Panagopoulos; +7 Authors

    Marine pollution from debris is a major issue nowadays, since every year large amounts of litter enter into the sea. Under the Horizon 2020 framework and within the Cleaning Litter by developing and Applying Innovative Methods in European Seas (CLAIM) project, innovative devices were designed, developed, tested and applied in laboratory and in the field. These consisted of a system named CLEAN TRASH for the prevention of macrolitter in river estuaries before entering the Sea and a filtering system for microplastics (MPs), to be placed at waste water treatment plants (WWTP). Laboratory experiments showed that macrolitters were blocked by 90% by the CLEAN TRASH system, while during the sea testing period at the Kifissos river estuary, a significant source of terrestrial based litter for the Saronikos Gulf, a total amount of 1,175 kg of litter was collected in 38 days before entering the sea, of which the 708 kg (60%) were plastic debris of various sizes and another 164 kg (14%) of styrofoam parts. The lab scale prototype of the filtering system for MPs had an efficiency of about 95%. The upscaled device was tested at the Megara WWTP and was able to withhold a significant amount of MPs. The theoretical contribution of such devices toward the reduction of plastic pollution in the Saronikos Gulf area and the Natura conservation areas therein, was also studied with the use of a 3-D coupled Hydrodynamic-Lagrangian litter tracking model. In all experiments performed, the installation of the above devices for a period of 2 years, resulted in a microplastics reduction by about 87% and a macroplastics reduction ranging from 13 to 43%, depending on the sources.

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    Frontiers in Marine Science
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      Frontiers in Marine Science
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    Authors: Garcia-Souto, Daniel; Diaz-Costas, Seila; Bruzos, Alicia L; Rocha, Sara; +14 Authors

    We performed whole-genome sequencing on 23 samples from 16 clam specimens, which includes eight neoplastic and eight non-neoplastic animals (Table 1), with Illumina paired-end libraries of 350 bp insert size and reads 150 bp long. Then, we run MITObim v1.9.1 (Hahn, et al. 2013) to assemble the full mitochondrial genome of all sequenced samples, using gene baits from the following Cox1 and 16S reference genes to prime the assembly of clam mitochondrial genomes: V. verrucosa (Cox1, with GenBank accession number KC429139, 16S: C429301), C. gallina (Cox1: KY547757, 16S: KY547777) and C. striatula (Cox1: KY547747, 16S: KY547767). The draft sequences were polished twice with Pilon v1.23 (Walker, et al. 2014), and conflictive repetitive fragments from the mitochondrial control region were resolved using long read sequencing with Oxford Nanopore technologies (ONT) on a set of representative samples from each species and tumours. ONT reads were assembled with Miniasm v0.3 (Li 2016) and corrected using Racon v1.3.1 (Vaser, et al. 2017). Protein-coding genes, rDNAs and tRNAs were annotated on the curated mitochondrial genomes using MITOS2 web server (Bernt, et al. 2013), and manually curated to fit ORFs as predicted by ORF-FINDER (Rombel, et al. 2002). The rebuilt sequences can be found here in VVE_CGA_Mitochondrial_DNA.fasta and the annotations in VVE_CGA_Mitochondrial_DNA.gff. We then mapped the paired-end sequencing data from healthy and neoplastic tissues from all neoplastic samples onto the V. verrucosa and C. gallina reference mitochondrial genomes using BWA-mem v0.7.17-r1188 (Li and Durbin 2009) with default parameters. Duplicate reads were marked with Picard 2.18.14 and removed from the analysis. The employed reference genome can be found in Ref_CGA_VVE.fa, and each bam file corresponds to a given animal (i.e. PLVV18_2249F-N0-alnCGA_VVE.sorted.detup.bam) in which the code represents the country (P, Portugal), and the locality (L, Lisbon) of procedence, the species (VV, Venus verrucosa), the year of collection (18, 2018), an internal code of the animal (2249) and the sequenced tissue (F, Foot; Also H from Haemolymph and G from Gill). Some of them were obtained from Whole genome amplified samples (WGA). There is a reference to the intensity of the neoplasia detected in the animal (N0=Healthy; N1, N2, N3 = different levels of neoplasia; N? = neoplasia but level unknown). COI Veneridae sequences were recovered from Genbank and Boldsystems and aligned with our mitochondria reconstructions and are in the COX_all_Venerids.phy file. This was later employed to reconstruct a molecular ML phylogeny shown as supplementary data in our manuscript. DEAH12 and TFIIH sequences, alignments and molecular phylogenies can be found here as well (alignments and trees). Satellite monomer clusters CL04 and CL17 reconstructions as recovered from repeatexplorer (Novak et al. 2010) from C. gallina NGS data can be found at "Satellite_references.fasta" and coverage stats for each of the specimens with NGS data here is present in Satellite_coverage.txt. Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukemia-like transmissible cancers, called hemic neoplasias, have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight V. verrucosa clams that were diagnosed with hemic neoplasia, from two sampling points located more than 1,000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing of tumour tissues from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukemia originated in C. gallina (or a closely related taxa) and was later transmitted to V. verrucosa, in which it survived as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all the studied tumours belonging to a single neoplastic C. gallina lineage that spread in the Seas of Southern Europe.

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    Authors: Sandven, Stein; Higgins, Ruth;

    This booklet provides a summary of the scientific research carried out on the INTAROS project from 2016-2021, towards an Integrated Arctic Observing System

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    Authors: Royston, Sam; Brady, Aoibheann; Chuter, Stephen J; Vishwakarma, Bramha D; +3 Authors

    eLightning presentation at AGU Fall Meeting 2021, online, 13-17 December 2021, New Orleans

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    Authors: O'Donncha, Fearghal; Akhriev, Albert; Eck, Bradley; Burke, Meredith; +2 Authors

    Machine learning has not achieved the same degree of success in environmental applications as in other industries. Challenges around data sparsity, quality, and consistency have limited the impact of deep neural network approaches and restricted the focus to research applications. An alternative approach -- that is more amenable to the characteristics of data coming from disparate IoT devices deployed at different times and locations in the ocean -- is to develop many lightweight models that can be readily scaled up or down based on the number of devices available at any time. This paper presents a serverless framework that naturally marries a single IoT sensor device with a forecasting model. Aspects related to data ingestion, data processing, model training and deployment are described. The framework is applied to a fish farm site in Atlantic Canada.

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    Authors: Koch, Marcus; Wolf, Eva;

    The data supplements contain: a) Supplementary Data Set 1 SupplementaryDataSet1_CytogeneticDataSurvey.xlsx This file contains 575 georeferenced chromosome counts and/or genome sizes across the Cochlearia genus. b) Supplementary Data Set 2 SupplementaryDataSet2_AccessionDetailsNGSdata.xlsx This file contains detailed information on 65 Cochlearia samples and 3 Ionopsidium samples included in NGS data generation and analysis. c) Supplementary Data Set 3 SupplementaryDataSet3_MetabolicCompoundMatrix.xlsx This file contains raw and normalized tables of 40 metabolic compounds consistently detected in all analyzed samples. d) Supplementary Data Set 4 SupplementaryDataSet4_FlowCytometrySummaryTable.xlsx This file contains detailed flow cytometry results. d) Supplementary Data Set 5 SupplementaryDataSet5_PlastomeAlignment.txt This file provides the plastome alignment as used for RAxML and BEAST analyses. e) Supplementary Data Set 6 SupplementaryDataSet6_PlastomePartitionfileRaxmlBEAST.txt This file contains data partitioning schemes for plastome RAxML and BEAST analyses. f) Supplementary Data Set 7 SupplementaryDataSet7_MitochondrialContigs.zip This folder contains annotated mitochondrial de novo consensus sequences of sample Cmica_0979 (in Genbank Flat File Format (*.gb)), as used as reference sequences in reference-based mappings and named as follows: SupplementaryDataSet7a.gb SupplementaryDataSet7b.gb SupplementaryDataSet7c.gb SupplementaryDataSet7d.gb SupplementaryDataSet7e.gb SupplementaryDataSet7f.gb SupplementaryDataSet7g.gb SupplementaryDataSet7h.gb g) Supplementary Data Set 8 SupplementaryDataSet8_MitochondrialGenomeAlignment.txt This file provides the alignment of mitochondrial genome sequences as inputted into RAxML analysis. h) Supplementary Data Set 9 SupplementaryDataSet9_nrSNPalignmentRAxML.phy This file provides the alignment of transcriptome-wide nuclear SNPs in phylip format as inputted into RAxML analysis. i) Supplementary Data Set 10 SupplementaryDataSet10_nrSNPsSplitstreeTreemix.vcf.zip This file provides hard-filtered biallelic transcriptome-wide nuclear SNPs in VCF format as used for SplitsTree and TreeMix analyses. j) Supplementary Data Set 11 SupplementaryDataSet11_nrSNPsStructure.txt This file provides the input for the STRUCTURE analysis of 62 Cochlearia samples. k) Supplementary Data Set 12 SupplementaryDataSet12_nrSNPsStructureBavarica.txt This file provides the input for the STRUCTURE analysis of Cochlearia bavarica. l) Supplementary Data Set 13 SupplementaryDataSet13_nrSNPsABC.vcf.gz This file provides the input for the ABC modelling in VCF format. With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This sudden change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed central carbon metabolism responses to cold in diverse species and ecotypes, likely due to continuous connections to cold habitats that may have facilitated widespread adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.

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    Authors: Jean-Baptiste Sallée; Violaine Pellichero; Camille Akhoudas; Etienne Pauthenet; +5 Authors

    This object includes two files. One (GlobalML_Trend_1970_2018.mat) contains the 1970-2018 trends of mixed-layer depth, 0-200 stratification, and pycnocline stratification, as described in: Sallée, J.B., Pellichero, V., Akhoudas, C., Pauthenet, E., Vignes, L., Schmidtko, S., Naveira Garabato, A., Sutherland, P., Kuusela, M., 2020, Fifty-year changes of the world ocean’s surface layer in response to climate change, 591, 592–598, https://doi.org/10.1038/s41586-021-03303-x. The second one (GlobalML_Climato_1970_2018.mat) contains a climatology of mixed-layer depth based on the same methodology as in Sallée et al., 2021 (nature; doi:https://doi.org/10.1038/s41586-021-03303-x) but without regressing a trend. The climatological field is therefore different than in the paper; more robust in region where trends are unphysical (e.g. winter high latitude)

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