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  • SDSN - Greece
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  • UK Research and Innovation
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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: Ana, Popovic; Tran, Hai; Anatoly, Tchigvintsev; Mahbod, Hajighasemi; +17 Authors

    AbstractMetagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.

    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/ Scientific Reportsarrow_drop_down
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    Scientific Reports
    Other literature type . Article . 2017 . Peer-reviewed
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    Europe PubMed Central
    Article . 2017
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    Article . 2017
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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/ Scientific Reportsarrow_drop_down
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      Scientific Reports
      Other literature type . Article . 2017 . Peer-reviewed
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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/
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      Article . 2017
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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      Article . 2017
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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: Forth, Jan H.; Forth, Leonie F.; Lycett, Samantha; Bell-Sakyi, Lesley; +8 Authors

    Additional file 5: Supplementary Appendix. Phylogenetic and molecular clock analyses of ASFLI-elements from different tick genomes and ASFV using different clock-rates and substitution models implemented in BEAST. Supplementary Appendix. Figure A1-A5, Tables A1-A7. FigA1- Phylogenetic tree of ASFV and ASFLI-elements. FigA2 – Phylogenetic tree of NCLDV including ASFV and ASFLI-elements. FigA3 – Time-scaled tree for partial EP1242L sequences from tick samples and reference ASFV (non-integrated). FigA4 - Time-scaled tree for partial EP1242L sequences from tick samples only (5e-7 substitutions per site per year). FigA5 - Time-scaled tree for partial EP1242L sequences from tick samples (1e-8 substitutions per site and year). Table A1 - Summary of EP1242L fragments derived from ticks and the tick cell line OME/CTVM21 (OME21) used in the analysis. Table A2 - Indels in the tick sample sequences relative to the start of EP1242L in ASFV|KM111295|Kenya|Ken06/Bus|2006. Table A3 - Estimated root height and overall mean clock rate for strict clocks with fixed priors. Table A4 - Estimated root height and overall (averaged over all branches) mean clock rate for relaxed clocks with fixed priors of the rate of the relaxed clock (some variation). Table A5 - Estimated root height and overall (averaged over all branches) mean clock rate for relaxed clocks with normal or log-normal priors on the rate of the relaxed clock (most variation). Table A6 - Estimated root height and overall (averaged over all branches) mean clock rate for strict clocks with log-normal priors on the rate of the strict clock for the five ASFV-like sequences from tick samples only. Table A7 - Marginal likelihood estimation using Path Sampling and Stepping Stone Sampling, showing that the log-normal clock rate prior with mean = 5e-7 is best, but not significantly better than the other clock rates.

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    Authors: Forth, Jan H.; Forth, Leonie F.; Lycett, Samantha; Bell-Sakyi, Lesley; +8 Authors

    Additional file 20: Figure S7. BLAST-analysis for identification of ASFLI-element containing contigs and annotation. 66,745 SPAdes assembled contigs were blasted (BLASTn, NCBI, v2.6.0+) against a customised database comprising all sequences with the NCBI taxonomy ID 10497 (African swine fever virus) (as of 16 January 2018). Hits were filtered using a cut off e-value of 1x10-4 and a minimum alignment length of 150 bp, resulting in 34 contigs. These were then blasted against the complete NCBI database (The non-redundant nucleotide collection) to reliably identify and annotate ASFV-like sequences and areas of the host genome using default parameters. BLASTp search of >500 bp ORFs was performed against the “Non-redundant protein sequences” database using default parameters.

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    Authors: I P, Holman; C, Brown; V, Janes; D, Sandars;

    The global land system is facing unprecedented pressures from growing human populations and climatic change. Understanding the effects these pressures may have is necessary to designing land management strategies that ensure food security, ecosystem service provision and successful climate mitigation and adaptation. However, the number of complex, interacting effects involved makes any complete understanding very difficult to achieve. Nevertheless, the recent development of integrated modelling frameworks allows for the exploration of the co-development of human and natural systems under scenarios of global change, potentially illuminating the main drivers and processes in future land system change. Here, we use one such integrated modelling framework (the CLIMSAVE Integrated Assessment Platform) to investigate the range of projected outcomes in the European land system across climatic and socio-economic scenarios for the 2050s. We find substantial consistency in locations and types of change even under the most divergent conditions, with results suggesting that climate change alone will lead to a contraction in the agricultural and forest area within Europe, particularly in southern Europe. This is partly offset by the introduction of socioeconomic changes that change both the demand for agricultural production, through changing food demand and net imports, and the efficiency of agricultural production. Simulated extensification and abandonment in the Mediterranean region is driven by future decreases in the relative profitability of the agricultural sector in southern Europe, owing to decreased productivity as a consequence of increased heat and drought stress and reduced irrigation water availability. The very low likelihood (< 33% probability) that current land use proportions in many parts of Europe will remain unchanged suggests that future policy should seek to promote and support the multifunctional role of agriculture and forests in different European regions, rather than focusing on increased productivity as a route to agricultural and forestry viability. Highlights • Future European land systems modelled across scenario space. • Substantial consistency in locations and types of change even under divergent conditions • Currently marginal agricultural areas may face complex and difficult choices.

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    Europe PubMed Central
    Article . 2017
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    Authors: Fereidouni, Sasan; Freimanis, Graham L.; Orynbayev, Mukhit; Ribeca, Paolo; +8 Authors

    In 2015, a mass die-off of ≈200,000 saiga antelopes in central Kazakhstan was caused by hemorrhagic septicemia attributable to the bacterium Pasteurella multocida serotype B. Previous analyses have indicated that environmental triggers associated with weather conditions, specifically air moisture and temperature in the region of the saiga antelope calving during the 10-day period running up to the event, were critical to the proliferation of latent bacteria and were comparable to conditions accompanying historically similar die-offs in the same areas. We investigated whether additional viral or bacterial pathogens could be detected in samples from affected animals using 3 different high-throughput sequencing approaches. We did not identify pathogens associated with commensal bacterial opportunisms in blood, kidney, or lung samples and thus concluded that P. multocida serotype B was the primary cause of the disease.

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    Emerging Infectious Diseases
    Other literature type . Article . 2019 . Peer-reviewed
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      Emerging Infectious Diseases
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      Europe PubMed Central
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      Emerging Infectious Diseases
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    Authors: Diego Robledo; Juan A. Rubiolo; Santiago Cabaleiro; Paulino Martínez; +1 Authors

    Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle. Brain expression differences were smaller and not associated with major growth-related genes, but with regulation of feeding-related sensory pathways. Further, SNP variants showing frequency differences between fast- and slow-growing fish pointed to genomic regions likely involved in growth regulation, and three of them were individually validated through SNP typing. Although different mechanisms appear to explain growth differences among families, general mechanisms seem also to be involved, and thus, results provide a set of useful candidate genes and markers to be evaluated for more efficient growth breeding programs and to perform comparative genomic studies of growth in fish and vertebrates This work was funded by Spanish Ministry of Economy and Competitiveness and European Regional Development Funds (AGL2012-35904), Ministry of Science and Innovation (Consolider Ingenio, Aquagenomics, CSD2007-00002), and Local Government. Xunta de Galicia (GRC2014/010). DR was supported by a FPU fellowship funded by Spanish Ministry of Education, Culture and Sport (AP2012-0254) and a postdoctoral contract funded by the Biotechnology and Biological Science Research Council (BBSRC) grant BB/N024044/1 SI

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    Europe PubMed Central
    Article . 2017
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    Scientific Reports
    Article . 2017
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    Scientific Reports
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    Scientific Reports
    Article . 2017 . Peer-reviewed
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      Scientific Reports
      Article . 2017 . Peer-reviewed
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    Authors: Forth, Jan H.; Forth, Leonie F.; Lycett, Samantha; Bell-Sakyi, Lesley; +8 Authors

    Additional file 7: Table S6. BLASTn results of SPAdes-assembled contigs from Ornithodoro porcinus France and Kenya17 containing ASFLI-elements. Shown are hits with the lowest e-value for ASFV-genes as obtained by Blastn against the entire NCBI database.

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    Authors: Fernandez, Carolina; Mascolo, Dario; Monaghan, Sean J.; Baily, Johanna L.; +5 Authors

    AbstractTwo aqueous fixation methods (modified Davidson's solution and modified Davidson's solution with 2% (w/v) Alcian blue) were compared against two non‐aqueous fixation methods (methacarn solution and methacarn solution with 2% (w/v) Alcian blue) along with the standard buffered formalin fixation method to (a) improve preservation of the mucous coat on Atlantic salmon, Salmo salar L., gills and (b) to examine the interaction between the amoebae and mucus on the gill during an infection with amoebic gill disease. Aqueous fixatives demonstrated excellent cytological preservation but failed to deliver the preservation of the mucus when compared to the non‐aqueous‐based fixatives; qualitative and semi‐quantitative analysis revealed a greater preservation of the gill mucus using the non‐aqueous methacarn solution. A combination of this fixation method and an Alcian blue/Periodic acid–Schiff staining was tested in gills of Atlantic salmon infected with amoebic gill disease; lectin labelling was also used to confirm the mucus preservation in the methacarn‐fixed tissue. Amoebae were observed closely associated with the mucus demonstrating that the techniques employed for preservation of the mucous coat can indeed avoid the loss of potential mucus‐embedded parasites, thus providing a better understanding of the relationship between the mucus and parasite.

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    Journal of Fish Diseases
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    Journal of Fish Diseases
    Other literature type . Article . 2019 . Peer-reviewed
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      Journal of Fish Diseases
      Other literature type . Article . 2019 . Peer-reviewed
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    Authors: De Ferrari, Luna; Mitchell, John BO;

    Background: In this work we predict enzyme function at the level of chemical mechanism, providing a finer granularity of annotation than traditional Enzyme Commission (EC) classes. Hence we can predict not only whether a putative enzyme in a newly sequenced organism has the potential to perform a certain reaction, but how the reaction is performed, using which cofactors and with susceptibility to which drugs or inhibitors, details with important consequences for drug and enzyme design. Work that predicts enzyme catalytic activity based on 3D protein structure features limits the prediction of mechanism to proteins already having either a solved structure or a close relative suitable for homology modelling. Results: In this study, we evaluate whether sequence identity, InterPro or Catalytic Site Atlas sequence signatures provide enough information for bulk prediction of enzyme mechanism. By splitting MACiE (Mechanism, Annotation and Classification in Enzymes database) mechanism labels to a finer granularity, which includes the role of the protein chain in the overall enzyme complex, the method can predict at 96% accuracy (and 96% micro-averaged precision, 99.9% macro-averaged recall) the MACiE mechanism definitions of 248 proteins available in the MACiE, EzCatDb (Database of Enzyme Catalytic Mechanisms) and SFLD (Structure Function Linkage Database) databases using an off-theshelf K-Nearest Neighbours multi-label algorithm. Conclusion: We find that InterPro signatures are critical for accurate prediction of enzyme mechanism. We also find that incorporating Catalytic Site Atlas attributes does not seem to provide additional accuracy. The software code (ml2db), data and results are available online at http://sourceforge.net/projects/ml2db/ and as supplementary files. Publisher PDF Peer reviewed

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    Europe PubMed Central
    Article . 2014
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    St Andrews Research Repository
    Article . 2014 . Peer-reviewed
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    BMC Bioinformatics
    Article . 2014 . Peer-reviewed
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    Authors: Catherine, Gibbons; Phillipa, Caudwell; Graham, Finlayson; Dominic-Luc, Webb; +3 Authors

    The relationship between postprandial peptides at circulating physiological levels and short-term appetite control is not well understood.The purpose of this study was first to compare the postprandial profiles of ghrelin, glucagon-like peptide 1 (GLP-1), and peptide YY (PYY) after isoenergetic meals differing in fat and carbohydrate content and second to examine the relationships between ghrelin, GLP-1, and PYY with hunger, fullness, and energy intake.Plasma was collected before and periodically after the meals for 180 minutes, after which time ad libitum food was provided. Simultaneous ratings of hunger and fullness were tracked for 180 minutes through phases identified as early (0-60 minutes) and late (60-180 minutes) satiety.This study was conducted at the Psychobiology and Energy Balance Research Unit, University of Leeds.The participants were 16 healthy overweight/obese adults.Changes in hunger and fullness and metabolic markers were indicators of the impact of the meals on satiety.Ghrelin was influenced similarly by the 2 meals [F(1, 12) = 0.658, P = .433] and was significantly associated with changes in hunger (P.05), which in turn correlated with food intake (P.05). GLP-1 and PYY increased more by the high-fat meal [F(1, 15) = 5.099 and F(1, 14) = 5.226, P.05]. GLP-1 was negatively associated with hunger in the late satiety phase and with energy intake (P.05), but the PYY profile was not associated with hunger or fullness, nor was PYY associated with food intake.The results demonstrate that under these conditions, these peptides respond differently to ingested nutrients. Ghrelin and GLP-1, but not PYY, were associated with short-term control of appetite over the measurement period.

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    The Journal of Clinical Endocrinology & Metabolism
    Other literature type . Article . 2013 . Peer-reviewed
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      The Journal of Clinical Endocrinology & Metabolism
      Other literature type . Article . 2013 . Peer-reviewed
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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: Ana, Popovic; Tran, Hai; Anatoly, Tchigvintsev; Mahbod, Hajighasemi; +17 Authors

    AbstractMetagenomics has made accessible an enormous reserve of global biochemical diversity. To tap into this vast resource of novel enzymes, we have screened over one million clones from metagenome DNA libraries derived from sixteen different environments for carboxylesterase activity and identified 714 positive hits. We have validated the esterase activity of 80 selected genes, which belong to 17 different protein families including unknown and cyclase-like proteins. Three metagenomic enzymes exhibited lipase activity, and seven proteins showed polyester depolymerization activity against polylactic acid and polycaprolactone. Detailed biochemical characterization of four new enzymes revealed their substrate preference, whereas their catalytic residues were identified using site-directed mutagenesis. The crystal structure of the metal-ion dependent esterase MGS0169 from the amidohydrolase superfamily revealed a novel active site with a bound unknown ligand. Thus, activity-centered metagenomics has revealed diverse enzymes and novel families of microbial carboxylesterases, whose activity could not have been predicted using bioinformatics tools.

    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/ Scientific Reportsarrow_drop_down
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    Scientific Reports
    Other literature type . Article . 2017 . Peer-reviewed
    License: CC BY
    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/
    Europe PubMed Central
    Article . 2017
    Data sources: PubMed Central
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    CNR ExploRA
    Article . 2017
    Data sources: CNR ExploRA
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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/ Scientific Reportsarrow_drop_down
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      Scientific Reports
      Other literature type . Article . 2017 . Peer-reviewed
      License: CC BY
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      Europe PubMed Central
      Article . 2017
      Data sources: PubMed Central
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      CNR ExploRA
      Article . 2017
      Data sources: CNR ExploRA
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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: Forth, Jan H.; Forth, Leonie F.; Lycett, Samantha; Bell-Sakyi, Lesley; +8 Authors

    Additional file 5: Supplementary Appendix. Phylogenetic and molecular clock analyses of ASFLI-elements from different tick genomes and ASFV using different clock-rates and substitution models implemented in BEAST. Supplementary Appendix. Figure A1-A5, Tables A1-A7. FigA1- Phylogenetic tree of ASFV and ASFLI-elements. FigA2 – Phylogenetic tree of NCLDV including ASFV and ASFLI-elements. FigA3 – Time-scaled tree for partial EP1242L sequences from tick samples and reference ASFV (non-integrated). FigA4 - Time-scaled tree for partial EP1242L sequences from tick samples only (5e-7 substitutions per site per year). FigA5 - Time-scaled tree for partial EP1242L sequences from tick samples (1e-8 substitutions per site and year). Table A1 - Summary of EP1242L fragments derived from ticks and the tick cell line OME/CTVM21 (OME21) used in the analysis. Table A2 - Indels in the tick sample sequences relative to the start of EP1242L in ASFV|KM111295|Kenya|Ken06/Bus|2006. Table A3 - Estimated root height and overall mean clock rate for strict clocks with fixed priors. Table A4 - Estimated root height and overall (averaged over all branches) mean clock rate for relaxed clocks with fixed priors of the rate of the relaxed clock (some variation). Table A5 - Estimated root height and overall (averaged over all branches) mean clock rate for relaxed clocks with normal or log-normal priors on the rate of the relaxed clock (most variation). Table A6 - Estimated root height and overall (averaged over all branches) mean clock rate for strict clocks with log-normal priors on the rate of the strict clock for the five ASFV-like sequences from tick samples only. Table A7 - Marginal likelihood estimation using Path Sampling and Stepping Stone Sampling, showing that the log-normal clock rate prior with mean = 5e-7 is best, but not significantly better than the other clock rates.

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    Other literature type . 2020
    License: CC BY
    Data sources: Datacite
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