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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: Munck, Nanna; Leekitcharoenphon, Pimlapas; Litrup, Eva; Kaas, Rolf; +12 Authors

    Zoonotic Salmonella causes millions of human salmonellosis infections worldwide each year. Information about the source of the bacteria guides risk managers on control and preventive strategies. Source attribution is the effort to quantify the number of sporadic human cases of a specific illness to specific sources and animal reservoirs. Source attribution methods for Salmonella have so far been based on traditional wet-lab typing methods. With the change to whole genome sequencing there is a need to develop new methods for source attribution based on sequencing data. Four European datasets collected in Denmark (DK), Germany (DE), the United Kingdom (UK) and France (FR) are presented in this descriptor. The datasets contain sequenced samples of Salmonella Typhimurium and its monophasic variants isolated from human, food, animal and the environment. The objective of the datasets was either to attribute the human salmonellosis cases to animal reservoirs or to investigate contamination of the environment by attributing the environmental isolates to different animal reservoirs. Measurement(s)sequence_assembly • DNATechnology Type(s)sequence assembly process • DNA sequencing • Paired-End SequencingFactor Type(s)geographic location • Salmonella Typhimurium isolate sourceSample Characteristic - OrganismSalmonellaSample Characteristic - LocationKingdom of Denmark • Germany • United Kingdom • French Republic Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11816748

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    Scientific Data
    Article . 2020 . Peer-reviewed
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    Europe PubMed Central
    Article . 2020
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    https://doi.org/10.25646/6582...
    Article . 2020
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      Article . 2020 . Peer-reviewed
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      https://doi.org/10.25646/6582...
      Article . 2020
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    Authors: Strubbia, Sofia; Phan, My V.T.; Schaeffer, JulieN; Koopmans, MarioN; +2 Authors

    This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.

    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/ NARCIS; Food and Env...arrow_drop_down
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    Food and Environmental Virology
    Other literature type . Article . 2019 . Peer-reviewed
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    Europe PubMed Central
    Article . 2019
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    Food and Environmental Virology
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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/ NARCIS; Food and Env...arrow_drop_down
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      Food and Environmental Virology
      Other literature type . Article . 2019 . Peer-reviewed
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      Europe PubMed Central
      Article . 2019
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    Authors: Pierre-Eric Campos; Emmanuel Pichon; Céline Moriou; Patricia Clerc; +6 Authors

    -N-methylaplysinopsin (7). Their structures were elucidated by 1D and 2D NMR spectra and HRESIMS data. All compounds were evaluated for their antimicrobial and their antiplasmodial activities. Regarding antimicrobial activities, the best compounds are (2) and (3), with minimum inhibitory concentration (MIC) of 0.01 and 1 µ Chemical study of the CH2Cl2-MeOH (1:1) extract of the sponge Fascaplysinopsis reticulata collected in Mayotte highlighted three new tryptophan derived alkaloids, 6,6&prime -dihydro-isoplysin A (3), along with the synthetically known 8-oxo-tryptamine (4) and the three known molecules from the same family, tryptamine (5), (E)-6-bromo-2&prime -N-methylaplysinopsin (7) showed moderate antiplasmodial activity against Plasmodium falciparum with IC50 values of 8.8 and 8.0 µ g/mL towards Vibrio carchariae. In addition the known 8-oxo-tryptamine (4) and the mixture of the (E)-6-bromo-2&prime g/mL, respectively, towards Vibrio natrigens, and (5), with MIC values of 1 µ -dihydro-isoplysin A (2) and 5,6-dibromo-8,1&prime -bis-(debromo)-gelliusine F (1), 6-bromo-8,1&prime -N-methylaplysinopsin (6) and (Z)-6-bromo-2&prime g/mL, respectively. -demethyl-3&prime

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    Article . 2019
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      Marine Drugs
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      Article . 2019
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    Authors: Seiliez, Iban; Belghit, Ikram; Yujie Gao; Skiba-Cassy, Sandrine; +7 Authors

    International audience; Monitoring autophagic flux in vivo or in organs remains limited and the ideal methods relative to the techniques possible with cell culture may not exist. Recently, a few papers have demonstrated the feasibility of measuring autophagic flux in vivo by intraperitoneal (IP) injection of pharmacological agents (chloroquine, leupeptin, vinblastine, and colchicine). However, the metabolic consequences of the administration of these drugs remain largely unknown. Here, we report that 0.8~mg/kg/day IP colchicine increased LC3-II protein levels in the liver of fasted trout, supporting the usefulness of this drug for studying autophagic flux in vivo in our model organism. This effect was accompanied by a decrease of plasma glucose concentration associated with a fall in the mRNA levels of gluconeogenesis-related genes. Concurrently, triglycerides and lipid droplets content in the liver increased. In contrast, transcript levels of β-oxidation-related gene Cpt1a dropped significantly. Together, these results match with the reported role of autophagy in the regulation of glucose homeostasis and intracellular lipid stores, and highlight the importance of considering these effects when using colchicine as an in vivo "autophagometer."

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    Europe PubMed Central
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    Presentation . 2016
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    Autophagy
    Article
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    Autophagy
    Article . 2016 . Peer-reviewed
    Data sources: Crossref
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      Autophagy
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      Autophagy
      Article . 2016 . Peer-reviewed
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    Authors: Leventakou, Vasiliki; Roumeliotaki, Theano; Martinez, David; Barros, Henrique; +43 Authors

    To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access. Fish is a rich source of essential nutrients for fetal development, but in contrast, it is also a well-known route of exposure to environmental pollutants. We assessed whether fish intake during pregnancy is associated with fetal growth and the length of gestation in a panel of European birth cohort studies. The study sample of 151,880 mother-child pairs was derived from 19 population-based European birth cohort studies. Individual data from cohorts were pooled and harmonized. Adjusted cohort-specific effect estimates were combined by using a random- and fixed-effects meta-analysis. Women who ate fish >1 time/wk during pregnancy had lower risk of preterm birth than did women who rarely ate fish (≤ 1 time/wk); the adjusted RR of fish intake >1 but 1 but <3 times/wk and 15.2 g (95% CI: 8.9, 21.5 g) for ≥ 3 times/wk independent of gestational age. The association was greater in smokers and in overweight or obese women. Findings were consistent across cohorts. This large, international study indicates that moderate fish intake during pregnancy is associated with lower risk of preterm birth and a small but significant increase in birth weight. info:eu-repo/grantAgreement/EC/FP7/241604, Special Research Account of University of Crete Netherlands Organisation for Health Research and Development and Nutricia Research Danish Council for Strategic Research 09-067124 March of Dimes Birth Defects Foundation Danish Heart Association Danish Medical Research Council Sygekassemes Helsefond Danish National Research Foundation Danish Pharmaceutical Association Ministry of Health National Board of Health Statens Serum Institut Fondation pour la Recherche Medicate French Ministry of Research: IFR program Institut National de la Sante et de la Recherche Medicate Nutrition Research program French Ministry of Health Perinatality Program French Agency for Environment security French National Institute for Population Health Surveillance Paris-Sud University, French National Institute for Health Education, Nestle Mutuelle Genarale de l'Education Nationale French speaking association for the study of diabetes and metabolism (Alfediam) National Agency for Research

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      Article . 2014
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      Article . 2014
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      Article . 2014
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      Article . 2014
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    Authors: Pérez-Sánchez, Jaume; Estensoro, Itziar; Redondo, Mª José; Calduch-Giner, Josep A.; +2 Authors

    Mucins are O-glycosylated glycoproteins present on the apex of all wet-surfaced epithelia with a well-defined expression pattern, which is disrupted in response to a wide range of injuries or challenges. The aim of this study was to identify mucin gene sequences of gilthead sea bream (GSB), to determine its pattern of distribution in fish tissues and to analyse their transcriptional regulation by dietary and pathogenic factors. Exhaustive search of fish mucins was done in GSB after de novo assembly of next-generation sequencing data hosted in the IATS transcriptome database (www.nutrigroup-iats.org/seabreamdb). Six sequences, three categorized as putative membrane-bound mucins and three putative secreted-gel forming mucins, were identified. The transcriptional tissue screening revealed that Muc18 was the predominant mucin in skin, gills and stomach of GSB. In contrast, Muc19 was mostly found in the oesophagus and Muc13 was along the entire intestinal tract, although the posterior intestine exhibited a differential pattern with a high expression of an isoform that does not share a clear orthologous in mammals. This mucin was annotated as intestinal mucin (I-Muc). Its RNA expression was highly regulated by the nutritional background, whereas the other mucins, including Muc2 and Muc2-like, were expressed more constitutively and did not respond to high replacement of fish oil (FO) by vegetable oils (VO) in plant protein-based diets. After challenge with the intestinal parasite Enteromyxum leei, the expression of a number of mucins was decreased mainly in the posterior intestine of infected fish. But, interestingly, the highest down-regulation was observed for the I-Muc. Overall, the magnitude of the changes reflected the intensity and progression of the infection, making mucins and I-Muc, in particular, reliable markers of prognostic and diagnostic value of fish intestinal health. © 2013 Pérez-Sánchez et al. This work was funded by the EU ARRAINA project (Advanced Research Initiatives for Nutrition & Aquaculture, FP7/2007/2013; grant agreement no. 288925) and by the Spanish Ministry of Science and Innovation (MICINN) through the projects AGL2009-13282-C02-01 and AQUAGENOMICS (CSD2007-00002, Improvement of Aquaculture Production by the Use of Biotechnological Tools). Additional funding was obtained from the >Generalitat Valenciana> (research grants PROMETEO 2010/006, ISIC 2011/003). Peer Reviewed

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    Europe PubMed Central
    Article . 2013
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      Article . 2013
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    Authors: Munck, Nanna; Leekitcharoenphon, Pimlapas; Litrup, Eva; Kaas, Rolf; +12 Authors

    Zoonotic Salmonella causes millions of human salmonellosis infections worldwide each year. Information about the source of the bacteria guides risk managers on control and preventive strategies. Source attribution is the effort to quantify the number of sporadic human cases of a specific illness to specific sources and animal reservoirs. Source attribution methods for Salmonella have so far been based on traditional wet-lab typing methods. With the change to whole genome sequencing there is a need to develop new methods for source attribution based on sequencing data. Four European datasets collected in Denmark (DK), Germany (DE), the United Kingdom (UK) and France (FR) are presented in this descriptor. The datasets contain sequenced samples of Salmonella Typhimurium and its monophasic variants isolated from human, food, animal and the environment. The objective of the datasets was either to attribute the human salmonellosis cases to animal reservoirs or to investigate contamination of the environment by attributing the environmental isolates to different animal reservoirs. Measurement(s)sequence_assembly • DNATechnology Type(s)sequence assembly process • DNA sequencing • Paired-End SequencingFactor Type(s)geographic location • Salmonella Typhimurium isolate sourceSample Characteristic - OrganismSalmonellaSample Characteristic - LocationKingdom of Denmark • Germany • United Kingdom • French Republic Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11816748

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    Scientific Data
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    Europe PubMed Central
    Article . 2020
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    https://doi.org/10.25646/6582...
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      https://doi.org/10.25646/6582...
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    Authors: Strubbia, Sofia; Phan, My V.T.; Schaeffer, JulieN; Koopmans, MarioN; +2 Authors

    This study aimed to optimize a method to identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of the viral capsid using pig-mucin capture or by selecting viral RNA prior to library preparation through a capture using the SureSelect target enrichment. The third method was based on a non-specific biophysical precipitation with polyethylene glycol. Full genomes of a number of common human enteric viruses including norovirus, rotavirus, husavirus, enterovirus and astrovirus were obtained. In stool samples full norovirus genome were detected as well as partial enterovirus genome. A variety of norovirus sequences was detected in sewage samples, with genogroup II being more prevalent. Interestingly, the pig-mucin capture enhanced not only the recovery of norovirus and rotavirus but also recovery of astrovirus, sapovirus and husavirus. Documenting sewage virome using these methods provides information for molecular epidemiology and may be useful in developing strategies to prevent further spread of viruses.

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    Food and Environmental Virology
    Other literature type . Article . 2019 . Peer-reviewed
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    Food and Environmental Virology
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    Authors: Pierre-Eric Campos; Emmanuel Pichon; Céline Moriou; Patricia Clerc; +6 Authors

    -N-methylaplysinopsin (7). Their structures were elucidated by 1D and 2D NMR spectra and HRESIMS data. All compounds were evaluated for their antimicrobial and their antiplasmodial activities. Regarding antimicrobial activities, the best compounds are (2) and (3), with minimum inhibitory concentration (MIC) of 0.01 and 1 µ Chemical study of the CH2Cl2-MeOH (1:1) extract of the sponge Fascaplysinopsis reticulata collected in Mayotte highlighted three new tryptophan derived alkaloids, 6,6&prime -dihydro-isoplysin A (3), along with the synthetically known 8-oxo-tryptamine (4) and the three known molecules from the same family, tryptamine (5), (E)-6-bromo-2&prime -N-methylaplysinopsin (7) showed moderate antiplasmodial activity against Plasmodium falciparum with IC50 values of 8.8 and 8.0 µ g/mL towards Vibrio carchariae. In addition the known 8-oxo-tryptamine (4) and the mixture of the (E)-6-bromo-2&prime g/mL, respectively, towards Vibrio natrigens, and (5), with MIC values of 1 µ -dihydro-isoplysin A (2) and 5,6-dibromo-8,1&prime -bis-(debromo)-gelliusine F (1), 6-bromo-8,1&prime -N-methylaplysinopsin (6) and (Z)-6-bromo-2&prime g/mL, respectively. -demethyl-3&prime

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