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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: Johan Gardères; Marie-Lise Bourguet-Kondracki; Bojan Hamer; Renato Batel; +2 Authors

    An overview on the diversity of 39 lectins from the phylum Porifera is presented, including 38 lectins, which were identified from the class of demosponges, and one lectin from the class of hexactinellida. Their purification from crude extracts was mainly performed by using affinity chromatography and gel filtration techniques. Other protocols were also developed in order to collect and study sponge lectins, including screening of sponge genomes and expression in heterologous bacterial systems. The characterization of the lectins was performed by Edman degradation or mass spectrometry. Regarding their physiological roles, sponge lectins showed to be involved in morphogenesis and cell interaction, biomineralization and spiculogenesis, as well as host defense mechanisms and potentially in the association between the sponge and its microorganisms. In addition, these lectins exhibited a broad range of bioactivities, including modulation of inflammatory response, antimicrobial and cytotoxic activities, as well as anticancer and neuromodulatory activity. In view of their potential pharmacological applications, sponge lectins constitute promising molecules of biotechnological interest.

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    Marine Drugs
    Article . 2015
    Data sources: DOAJ-Articles
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    Article . 2015
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    Marine Drugs
    Other literature type . Article . 2015 . Peer-reviewed
    License: CC BY
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    Marine Drugs
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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/ Europe PubMed Centra...arrow_drop_down
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      Marine Drugs
      Article . 2015
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      Marine Drugs
      Other literature type . Article . 2015 . Peer-reviewed
      License: CC BY
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      Marine Drugs
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    Authors: Thierry Burgeot; Farida Akcha; Dominique Ménard; Craig D. Robinson; +10 Authors

    The International workshop on Integrated Assessment of CONtaminants impacts on the North sea (ICON) provided a framework to validate the application of chemical and biological assessment thresholds (BACs and EACs) in the Seine Bay in France. Bioassays (oyster larval anomalies, Corophium arenarium toxicity assay and DR Calux) for sediment and biomarkers: ethoxyresorufin-O-deethylase (EROD) activity, acetylcholinesterase (AChE) activity, lysosomal membrane stability (LMS), DNA strand breaks using the Comet assay, DNA adducts, micronucleus (MN), PAH metabolites, imposex, intersex and fish external pathologies were analysed in four marine sentinel species (Platichthys flesus, Limanda limanda, Mytilus sp. and Nucella lapilus). Polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and heavy metals were analysed in biota and sediment. Results for sediment and four species in 2008–2009 made it possible to quantify the impact of contaminants using thresholds (Environmental Assessment Criteria/EAC2008: 70% and EAC2009: 60%) and effects (EAC2008: 50% and EAC2009: 40%) in the Seine estuary. The Seine estuary is ranked among Europe's most highly polluted sites. 1,953

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    Marine Environmental Research
    Article . 2017 . Peer-reviewed
    License: Elsevier TDM
    Data sources: Crossref
    Hal-Diderot
    Article . 2017
    Data sources: Hal-Diderot
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  • Authors: Zakoua Guédé; Alexandru Tantar; Emilia Tantar; Pierre Del Moral;

    The present study aims at investigating advanced subset simulation techniques, which are based on the theory of particle filter, for the assessment of the failure probability of a marine structure under extreme loading conditions. Three approaches are considered, namely the classical particle filter method, the subset simulation with a branching process and one using the minimum values of the samples as levels. They are, first, intensively applied on a simple example for which a known analytical solution is available, in order to investigate their parameter settings. Then, they are applied, with good performance, using their respective best parameter settings, to the assessment of failure probability of a FPSO subjected to extreme roll motion.

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    Authors: Perez, M.; Livoreil, B.; Mantovani, S.; Boisselier, M. C.; +11 Authors

    The Hermann's tortoise (Testudo hermanni) is an endangered land tortoise distributed in disjoint populations across Mediterranean Europe. We investigated its genetic variation by typing 1 mitochondrial locus and 9 nuclear microsatellites in approximately 300 individuals from 22 localities. Our goal was to understand the relative impact of natural and human-mediated processes in shaping the genetic structure and to identify the genetic priorities for the conservation of this species. We found that 1) all geographic areas are highly differentiated, mainly as a function of their distance but with a clear genetic discontinuity (F st values larger than 0.4) between the Eastern and the Western subspecies; 2) the contact zone between subspecies is located farthest to the west than previously believed, and it probably coincides with the delta of the largest Italian river; 3) extinction events due to climatic conditions in the Upper Palaeolithic and subsequent human-mediated translocations in the Neolithic possibly explain the unexpected similarity among Spain, Sicily, and Corsica. For conservation purposes, the large majority of genetic pools appears native although hybridization among subspecies, related to extensive 20th century trade of tortoises across Europe, is observed in Spain and some Italian samples. Most populations do not seem at immediate risk of low genetic variation, except the French population, which has very low nuclear genetic diversity (heterozygosity = 0.25) and where 50 out of 51 sampled animals shared the same mitochondrial sequence. In general, restocking and reintroduction plans should carefully consider the genetic background of the individuals.

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    Journal of Heredity
    Article . 2013 . Peer-reviewed
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    Authors: Oumar Traoré; Outi Nyholm; Anja Siitonen; Isidore Juste O. Bonkoungou; +3 Authors

    Background: This study investigated the prevalence, serotypes and antimicrobial sensitivity patterns of Salmonella enterica in environment in Ouagadougou, Burkina Faso. A total of 476 samples, consisting of 36 samples of tap water, 51 samples of well water, 87 samples of channel water, 44 samples of reservoir water, 238 samples of fish, and 20 samples of lettuce were examined using standard bacteriological procedures for Salmonella. Results: Salmonella were isolated from 98 samples. Salmonella were rare in drinking water, since they were not found at all from the tap water, and only in 2 % of well water. Salmonella were more common in the water of reservoir of Tanghin (15 %), reservoir of Yamtenga (20 %), and in the water channels in the city (from 20 to 31 %). Salmonella were commonly isolated from the fish (24 %) caught from the reservoir of Tanghin and from the lettuce (50 %) irrigated with water from Tanghin. The Salmonella isolates were found to represent 50 different serotypes. The 11 most common serotypes were Salmonella Bredeney and S. Colindale (both 8.2 %), S. Muenster (6.1 %), S. Korlebu (5.1 %), S. Eastbourne and S. Poona (both 4.1 %), and S. Agona, S. Derby, S. Drac, S. Senftenberg, S. Waycross (each 3.1 %), accounting for 51.3 % of all the isolates. In general, the Salmonella strains were sensitive to the antimicrobials tested, but two strains were resistant to streptomycin and many more intermediate to streptomycin or sulphonamide. Conclusion: This study highlights the common prevalence of Salmonella and the high diversity of Salmonella serotypes in aquatic environment in Ouagadougou, Burkina Faso. Therefore, various human activities linked to water and consumption of water-related products, such as fish and lettuce, can lead to human Salmonella infections. Peer reviewed

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    BMC Microbiology
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    BMC Microbiology
    Article . 2015 . Peer-reviewed
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      BMC Microbiology
      Article . 2015 . Peer-reviewed
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    Authors: Francesca Verones; Alya F. Bolowich; Keigo Ebata; Anukorn Boutson; +2 Authors

    Fish provides an important source of protein, especially in developing countries, and the amounts of fish consumed are increasing worldwide (mostly from aquaculture). More than half of all marine fish are caught by small-scale fishery operations. However, no life cycle assessment (LCA) of small-scale fisheries and no LCA of marine fishery operations in Asia (Thailand) exists today. We perform LCAs to compare the impacts of three different fishing techniques: crab gill-nets, squid traps, and fish traps. Primary data sourced from four different fishers were used. We distinguished the life cycle inventories for three different seasons (northeast monsoon, southwest monsoon and pre-monsoon), since the time spent on the water and catch varied significantly between the seasons. Our results showed the largest impacts from artisanal fishing operations affect climate change, human toxicity, and fossil and metal depletion. Our results are, in terms of global warming potential, comparable with other artisanal fisheries. Between different fishing operations, impacts vary between a factor of 2 (for land transformation impacts) and up to a factor of more than 20 (fossil fuel depletion and marine eutrophication). This shows that the way in which operations are performed have a very strong influence on results. Seasonality plays a relevant role for the assessment. Our results highlight that it is important to account for seasonal aspects in LCAs. We encourage a continual effort for collecting and modeling inventory processes, as well as making them available, in order to guarantee that LCA studies outside of Europe can be performed more easily. © 2017 The Author(s). This open access article is distributed under a Creative Commons Attribution (CC-BY) 4.0 license.

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    Cogent Environmental Science
    Article . 2017 . Peer-reviewed
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    NTNU Open
    Article . 2017
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      Cogent Environmental Science
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    Authors: Ferenc Jordán; Mario Lauria; Marco Scotti; Thanh Phuong Nguyen; +3 Authors

    AbstractCoexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.

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    OceanRep
    Article . 2015 . Peer-reviewed
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    Scientific Reports
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    Scientific Reports
    Article . 2015 . Peer-reviewed
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      OceanRep
      Article . 2015 . Peer-reviewed
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      Scientific Reports
      Article . 2015 . Peer-reviewed
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    Authors: Axelle Aimond; Kevin Calabro; Coralie Audoin; Elodie Olivier; +8 Authors

    International audience; This paper reports the isolation and structural characterization of four new ent-kaurane derivatives from the Lamiaceae plant Sideritis hyssopifolia. Planar structures and relative configurations were determined using both mass spectrometry and nuclear magnetic resonance (1D and 2D). Absolute configurations were determined by comparing experimental and theoretical electronic circular dichroism spectra. The cytotoxic and microbial activities of all new compounds were tested. Compounds that were non-cytotoxic were further evaluated for anti-inflammatory activity.

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    Molecules
    Other literature type . Article . 2020 . Peer-reviewed
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    Molecules
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    Molecules
    Article . 2020
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    DOAJ
    Article . 2020
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      Molecules
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      Molecules
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    Authors: Lai, Adelene; Singh, Randolph; Kovalova, Lubomira; Jaeggi, Oliver; +2 Authors

    Abstract BackgroundApplying non-target analysis (NTA) in regulatory environmental monitoring remains challenging - instead of having exploratory questions, regulators usually already have specific questions related to environmental protection aims. Additionally, data analysis can seem overwhelming because of the large data volumes and many steps required. This work aimed to identify environmental chemical unknowns via retrospective NTA within the scope of a pre-existing Swiss environmental monitoring campaign focusing on industrial chemicals. The research question addressed immediate regulatory priorities: identify pollutants with industrial point sources occurring at the highest intensities over two time points. Samples from 22 wastewater treatment plants obtained in 2018 and measured using liquid chromatography-high resolution mass spectrometry were retrospectively analysed by i) performing peak-picking to identify masses of interest, ii) prescreening and quality-controlling spectra, and iii) tentatively identifying priority “known unknown” pollutants by leveraging environmentally-relevant chemical information provided by Swiss, Swedish, EU-wide, and American regulators. This regulator-supplied information was incorporated into MetFrag, an in silico identification tool replete with “post-relaunch” features used here. This study’s unique regulatory context posed challenges in data quality and volume that were directly addressed with the prescreening, quality control, and identification workflow developed. ResultsOne confirmed and twenty-one tentative identifications were achieved, suggesting the presence of compounds as diverse as manufacturing reagents, adhesives, pesticides, and pharmaceuticals in the samples. More importantly, an in-depth interpretation of the results in the context of environmental regulation and actionable next steps are discussed. The prescreening and quality control workflow is openly accessible within the R package Shinyscreen, and adaptable to any (retrospective) analysis requiring automated quality control of mass spectra and non-target identification, with potential applications in environmental and metabolomics analyses. ConclusionsNTA in regulatory monitoring is critical for environmental protection, but bottlenecks in data analysis and results interpretation remain. The prescreening and quality control workflow, and interpretation work performed here are crucial steps towards scaling up NTA for environmental monitoring.

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    https://doi.org/10.21203/rs.3....
    Preprint . 2020
    License: CC BY
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    https://doi.org/10.17881/40ss-...
    Other literature type . 2021
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      https://doi.org/10.21203/rs.3....
      Preprint . 2020
      License: CC BY
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      https://doi.org/10.17881/40ss-...
      Other literature type . 2021
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    Authors: Begoña Talavera Andújar; Dagny Aurich; Velma T. E. Aho; Randolph R. Singh; +6 Authors

    Abstract Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease, with an increasing incidence in recent years due to the aging population. Genetic mutations alone only explain <10% of PD cases, while environmental factors, including small molecules, may play a significant role in PD. In the present work, 22 plasma (11 PD, 11 control) and 19 feces samples (10 PD, 9 control) were analyzed by non-target high-resolution mass spectrometry (NT-HRMS) coupled to two liquid chromatography (LC) methods (reversed-phase (RP) and hydrophilic interaction liquid chromatography (HILIC)). A cheminformatics workflow was optimized using open software (MS-DIAL and patRoon) and open databases (all public MSP-formatted spectral libraries for MS-DIAL, PubChemLite for Exposomics, and the LITMINEDNEURO list for patRoon). Furthermore, five disease-specific databases and three suspect lists (on PD and related disorders) were developed, using PubChem functionality to identifying relevant unknown chemicals. The results showed that non-target screening with the larger databases generally provided better results compared with smaller suspect lists. However, two suspect screening approaches with patRoon were also good options to study specific chemicals in PD. The combination of chromatographic methods (RP and HILIC) as well as two ionization modes (positive and negative) enhanced the coverage of chemicals in the biological samples. While most metabolomics studies in PD have focused on blood and cerebrospinal fluid, we found a higher number of relevant features in feces, such as alanine betaine or nicotinamide, which can be directly metabolized by gut microbiota. This highlights the potential role of gut dysbiosis in PD development. Michael J. Fox Foundation for Parkinson's Research http://dx.doi.org/10.13039/100000864 National Center for Biotechnology Information of the National Library of Medicine European Union’s Horizon 2020 research and innovation programme “Microbiomes in One Health” PhD training program Luxembourg National Research Fund Parkinson’s Foundation 100013301

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    Analytical and Bioanalytical Chemistry
    Article . 2022 . Peer-reviewed
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      Analytical and Bioanalytical Chemistry
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    Authors: Johan Gardères; Marie-Lise Bourguet-Kondracki; Bojan Hamer; Renato Batel; +2 Authors

    An overview on the diversity of 39 lectins from the phylum Porifera is presented, including 38 lectins, which were identified from the class of demosponges, and one lectin from the class of hexactinellida. Their purification from crude extracts was mainly performed by using affinity chromatography and gel filtration techniques. Other protocols were also developed in order to collect and study sponge lectins, including screening of sponge genomes and expression in heterologous bacterial systems. The characterization of the lectins was performed by Edman degradation or mass spectrometry. Regarding their physiological roles, sponge lectins showed to be involved in morphogenesis and cell interaction, biomineralization and spiculogenesis, as well as host defense mechanisms and potentially in the association between the sponge and its microorganisms. In addition, these lectins exhibited a broad range of bioactivities, including modulation of inflammatory response, antimicrobial and cytotoxic activities, as well as anticancer and neuromodulatory activity. In view of their potential pharmacological applications, sponge lectins constitute promising molecules of biotechnological interest.

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    Marine Drugs
    Article . 2015
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    Marine Drugs
    Other literature type . Article . 2015 . Peer-reviewed
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    Marine Drugs
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      Marine Drugs
      Article . 2015
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      Marine Drugs
      Other literature type . Article . 2015 . Peer-reviewed
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      Marine Drugs
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    Authors: Thierry Burgeot; Farida Akcha; Dominique Ménard; Craig D. Robinson; +10 Authors

    The International workshop on Integrated Assessment of CONtaminants impacts on the North sea (ICON) provided a framework to validate the application of chemical and biological assessment thresholds (BACs and EACs) in the Seine Bay in France. Bioassays (oyster larval anomalies, Corophium arenarium toxicity assay and DR Calux) for sediment and biomarkers: ethoxyresorufin-O-deethylase (EROD) activity, acetylcholinesterase (AChE) activity, lysosomal membrane stability (LMS), DNA strand breaks using the Comet assay, DNA adducts, micronucleus (MN), PAH metabolites, imposex, intersex and fish external pathologies were analysed in four marine sentinel species (Platichthys flesus, Limanda limanda, Mytilus sp. and Nucella lapilus). Polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and heavy metals were analysed in biota and sediment. Results for sediment and four species in 2008–2009 made it possible to quantify the impact of contaminants using thresholds (Environmental Assessment Criteria/EAC2008: 70% and EAC2009: 60%) and effects (EAC2008: 50% and EAC2009: 40%) in the Seine estuary. The Seine estuary is ranked among Europe's most highly polluted sites. 1,953

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    Marine Environmental Research
    Article . 2017 . Peer-reviewed
    License: Elsevier TDM
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    Article . 2017
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  • Authors: Zakoua Guédé; Alexandru Tantar; Emilia Tantar; Pierre Del Moral;

    The present study aims at investigating advanced subset simulation techniques, which are based on the theory of particle filter, for the assessment of the failure probability of a marine structure under extreme loading conditions. Three approaches are considered, namely the classical particle filter method, the subset simulation with a branching process and one using the minimum values of the samples as levels. They are, first, intensively applied on a simple example for which a known analytical solution is available, in order to investigate their parameter settings. Then, they are applied, with good performance, using their respective best parameter settings, to the assessment of failure probability of a FPSO subjected to extreme roll motion.

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    Authors: Perez, M.; Livoreil, B.; Mantovani, S.; Boisselier, M. C.; +11 Authors

    The Hermann's tortoise (Testudo hermanni) is an endangered land tortoise distributed in disjoint populations across Mediterranean Europe. We investigated its genetic variation by typing 1 mitochondrial locus and 9 nuclear microsatellites in approximately 300 individuals from 22 localities. Our goal was to understand the relative impact of natural and human-mediated processes in shaping the genetic structure and to identify the genetic priorities for the conservation of this species. We found that 1) all geographic areas are highly differentiated, mainly as a function of their distance but with a clear genetic discontinuity (F st values larger than 0.4) between the Eastern and the Western subspecies; 2) the contact zone between subspecies is located farthest to the west than previously believed, and it probably coincides with the delta of the largest Italian river; 3) extinction events due to climatic conditions in the Upper Palaeolithic and subsequent human-mediated translocations in the Neolithic possibly explain the unexpected similarity among Spain, Sicily, and Corsica. For conservation purposes, the large majority of genetic pools appears native although hybridization among subspecies, related to extensive 20th century trade of tortoises across Europe, is observed in Spain and some Italian samples. Most populations do not seem at immediate risk of low genetic variation, except the French population, which has very low nuclear genetic diversity (heterozygosity = 0.25) and where 50 out of 51 sampled animals shared the same mitochondrial sequence. In general, restocking and reintroduction plans should carefully consider the genetic background of the individuals.

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    Journal of Heredity
    Article . 2013 . Peer-reviewed
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    Authors: Oumar Traoré; Outi Nyholm; Anja Siitonen; Isidore Juste O. Bonkoungou; +3 Authors

    Background: This study investigated the prevalence, serotypes and antimicrobial sensitivity patterns of Salmonella enterica in environment in Ouagadougou, Burkina Faso. A total of 476 samples, consisting of 36 samples of tap water, 51 samples of well water, 87 samples of channel water, 44 samples of reservoir water, 238 samples of fish, and 20 samples of lettuce were examined using standard bacteriological procedures for Salmonella. Results: Salmonella were isolated from 98 samples. Salmonella were rare in drinking water, since they were not found at all from the tap water, and only in 2 % of well water. Salmonella were more common in the water of reservoir of Tanghin (15 %), reservoir of Yamtenga (20 %), and in the water channels in the city (from 20 to 31 %). Salmonella were commonly isolated from the fish (24 %) caught from the reservoir of Tanghin and from the lettuce (50 %) irrigated with water from Tanghin. The Salmonella isolates were found to represent 50 different serotypes. The 11 most common serotypes were Salmonella Bredeney and S. Colindale (both 8.2 %), S. Muenster (6.1 %), S. Korlebu (5.1 %), S. Eastbourne and S. Poona (both 4.1 %), and S. Agona, S. Derby, S. Drac, S. Senftenberg, S. Waycross (each 3.1 %), accounting for 51.3 % of all the isolates. In general, the Salmonella strains were sensitive to the antimicrobials tested, but two strains were resistant to streptomycin and many more intermediate to streptomycin or sulphonamide. Conclusion: This study highlights the common prevalence of Salmonella and the high diversity of Salmonella serotypes in aquatic environment in Ouagadougou, Burkina Faso. Therefore, various human activities linked to water and consumption of water-related products, such as fish and lettuce, can lead to human Salmonella infections. Peer reviewed

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    BMC Microbiology
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    BMC Microbiology
    Article . 2015 . Peer-reviewed
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      BMC Microbiology
      Article . 2015 . Peer-reviewed
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    Authors: Francesca Verones; Alya F. Bolowich; Keigo Ebata; Anukorn Boutson; +2 Authors

    Fish provides an important source of protein, especially in developing countries, and the amounts of fish consumed are increasing worldwide (mostly from aquaculture). More than half of all marine fish are caught by small-scale fishery operations. However, no life cycle assessment (LCA) of small-scale fisheries and no LCA of marine fishery operations in Asia (Thailand) exists today. We perform LCAs to compare the impacts of three different fishing techniques: crab gill-nets, squid traps, and fish traps. Primary data sourced from four different fishers were used. We distinguished the life cycle inventories for three different seasons (northeast monsoon, southwest monsoon and pre-monsoon), since the time spent on the water and catch varied significantly between the seasons. Our results showed the largest impacts from artisanal fishing operations affect climate change, human toxicity, and fossil and metal depletion. Our results are, in terms of global warming potential, comparable with other artisanal fisheries. Between different fishing operations, impacts vary between a factor of 2 (for land transformation impacts) and up to a factor of more than 20 (fossil fuel depletion and marine eutrophication). This shows that the way in which operations are performed have a very strong influence on results. Seasonality plays a relevant role for the assessment. Our results highlight that it is important to account for seasonal aspects in LCAs. We encourage a continual effort for collecting and modeling inventory processes, as well as making them available, in order to guarantee that LCA studies outside of Europe can be performed more easily. © 2017 The Author(s). This open access article is distributed under a Creative Commons Attribution (CC-BY) 4.0 license.

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    Cogent Environmental Science
    Article . 2017 . Peer-reviewed
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    NTNU Open
    Article . 2017
    Data sources: NTNU Open
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      Cogent Environmental Science
      Article . 2017 . Peer-reviewed
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      NTNU Open
      Article . 2017
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    Authors: Ferenc Jordán; Mario Lauria; Marco Scotti; Thanh Phuong Nguyen; +3 Authors

    AbstractCoexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.

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    OceanRep
    Article . 2015 . Peer-reviewed
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    Scientific Reports
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    Scientific Reports
    Article . 2015 . Peer-reviewed
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      OceanRep
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      Scientific Reports
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    Authors: Axelle Aimond; Kevin Calabro; Coralie Audoin; Elodie Olivier; +8 Authors

    International audience; This paper reports the isolation and structural characterization of four new ent-kaurane derivatives from the Lamiaceae plant Sideritis hyssopifolia. Planar structures and relative configurations were determined using both mass spectrometry and nuclear magnetic resonance (1D and 2D). Absolute configurations were determined by comparing experimental and theoretical electronic circular dichroism spectra. The cytotoxic and microbial activities of all new compounds were tested. Compounds that were non-cytotoxic were further evaluated for anti-inflammatory activity.

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    Molecules
    Other literature type . Article . 2020 . Peer-reviewed
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    Molecules
    Article . 2020
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    Authors: Lai, Adelene; Singh, Randolph; Kovalova, Lubomira; Jaeggi, Oliver; +2 Authors

    Abstract BackgroundApplying non-target analysis (NTA) in regulatory environmental monitoring remains challenging - instead of having exploratory questions, regulators usually already have specific questions related to environmental protection aims. Additionally, data analysis can seem overwhelming because of the large data volumes and many steps required. This work aimed to identify environmental chemical unknowns via retrospective NTA within the scope of a pre-existing Swiss environmental monitoring campaign focusing on industrial chemicals. The research question addressed immediate regulatory priorities: identify pollutants with industrial point sources occurring at the highest intensities over two time points. Samples from 22 wastewater treatment plants obtained in 2018 and measured using liquid chromatography-high resolution mass spectrometry were retrospectively analysed by i) performing peak-picking to identify masses of interest, ii) prescreening and quality-controlling spectra, and iii) tentatively identifying priority “known unknown” pollutants by leveraging environmentally-relevant chemical information provided by Swiss, Swedish, EU-wide, and American regulators. This regulator-supplied information was incorporated into MetFrag, an in silico identification tool replete with “post-relaunch” features used here. This study’s unique regulatory context posed challenges in data quality and volume that were directly addressed with the prescreening, quality control, and identification workflow developed. ResultsOne confirmed and twenty-one tentative identifications were achieved, suggesting the presence of compounds as diverse as manufacturing reagents, adhesives, pesticides, and pharmaceuticals in the samples. More importantly, an in-depth interpretation of the results in the context of environmental regulation and actionable next steps are discussed. The prescreening and quality control workflow is openly accessible within the R package Shinyscreen, and adaptable to any (retrospective) analysis requiring automated quality control of mass spectra and non-target identification, with potential applications in environmental and metabolomics analyses. ConclusionsNTA in regulatory monitoring is critical for environmental protection, but bottlenecks in data analysis and results interpretation remain. The prescreening and quality control workflow, and interpretation work performed here are crucial steps towards scaling up NTA for environmental monitoring.

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    https://doi.org/10.21203/rs.3....
    Preprint . 2020
    License: CC BY
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    https://doi.org/10.17881/40ss-...
    Other literature type . 2021
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      https://doi.org/10.21203/rs.3....
      Preprint . 2020
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      https://doi.org/10.17881/40ss-...
      Other literature type . 2021
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    Authors: Begoña Talavera Andújar; Dagny Aurich; Velma T. E. Aho; Randolph R. Singh; +6 Authors

    Abstract Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease, with an increasing incidence in recent years due to the aging population. Genetic mutations alone only explain <10% of PD cases, while environmental factors, including small molecules, may play a significant role in PD. In the present work, 22 plasma (11 PD, 11 control) and 19 feces samples (10 PD, 9 control) were analyzed by non-target high-resolution mass spectrometry (NT-HRMS) coupled to two liquid chromatography (LC) methods (reversed-phase (RP) and hydrophilic interaction liquid chromatography (HILIC)). A cheminformatics workflow was optimized using open software (MS-DIAL and patRoon) and open databases (all public MSP-formatted spectral libraries for MS-DIAL, PubChemLite for Exposomics, and the LITMINEDNEURO list for patRoon). Furthermore, five disease-specific databases and three suspect lists (on PD and related disorders) were developed, using PubChem functionality to identifying relevant unknown chemicals. The results showed that non-target screening with the larger databases generally provided better results compared with smaller suspect lists. However, two suspect screening approaches with patRoon were also good options to study specific chemicals in PD. The combination of chromatographic methods (RP and HILIC) as well as two ionization modes (positive and negative) enhanced the coverage of chemicals in the biological samples. While most metabolomics studies in PD have focused on blood and cerebrospinal fluid, we found a higher number of relevant features in feces, such as alanine betaine or nicotinamide, which can be directly metabolized by gut microbiota. This highlights the potential role of gut dysbiosis in PD development. Michael J. Fox Foundation for Parkinson's Research http://dx.doi.org/10.13039/100000864 National Center for Biotechnology Information of the National Library of Medicine European Union’s Horizon 2020 research and innovation programme “Microbiomes in One Health” PhD training program Luxembourg National Research Fund Parkinson’s Foundation 100013301

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    Analytical and Bioanalytical Chemistry
    Article . 2022 . Peer-reviewed
    License: CC BY
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      Analytical and Bioanalytical Chemistry
      Article . 2022 . Peer-reviewed
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