Investigation of MALDI-TOF Mass Spectrometry for Assessing the Molecular Diversity of Campylobacter jejuni and Comparison with MLST and cgMLST: A Luxembourg One-Health Study.

peer reviewedThere is a need for active molecular surveillance of human and veterinary Campylobacter infections. However, sequencing of all isolates is associated with high costs and a considerable workload. Thus, there is a need for a straightforward complementary tool to prioritize isolates to sequence. In this study, we proposed to investigate the ability of MALDI-TOF MS to pre-screen C. jejuni genetic diversity in comparison to MLST and cgMLST. A panel of 126 isolates, with 10 clonal complexes (CC), 21 sequence types (ST) and 42 different complex types (CT) determined by the SeqSphere+ cgMLST, were analysed by a MALDI Biotyper, resulting into one average spectra per isolate. Concordance and discriminating ability were evaluated based on protein profiles and different cut-offs. A random forest algorithm was trained to predict STs. With a 94% similarity cut-off, an AWC of 1.000, 0.933 and 0.851 was obtained for MLSTCC, MLSTST and cgMLST profile, respectively. The random forest classifier showed a sensitivity and specificity up to 97.5% to predict four different STs. Protein profiles allowed to predict C. jejuni CCs, STs and CTs at 100%, 93% and 85%, respectively. Machine learning and MALDI-TOF MS could be a fast and inexpensive complementary tool to give an early signal of recurrent C. jejuni on a routine basis

ATTEST - ICT Platform to enhance TSO/DSO coordination

<p>This project provides the integration infrastructure for the open-source toolbox, and it is used by the ICT Platform. It includes the tools integrated in the Platform, and the set of wrappers used by the Platform to run the tools. This program is free software: you can redistribute it and/or modify it under the terms of the European Union Public Licence v1.2 as published by the European Union.</p&gt

Study of intragastric structuring ability of sodium alginate based o/w emulsions under in vitro physiological pre-absorptive digestion conditions

In the present work, the intragastric structuring ability of o/w emulsions either stabilised (1–4%, w/w of sodium alginate (SA)) or structured with sheared ionic gel (1–3%, w/w of SA crosslinked with Ca2+) in the absence (saliva and gastric phases constituted of deionised water) or presence of in vitro pre-absorptive conditions (physiological simulated saliva and gastric fluids) was investigated. Visualisation of the morphological aspects of the gastric chymes, in the absence of multivalent counterions, demonstrated that SA stabilised systems underwent a remarkable swelling in the pH range of 2–3, whilst at the same pH range, ionic SA gel structured systems maintained their major structure configuration. When the aforementioned systems were exposed to physiological intragastric fluids, a reduction of the length and the hydrodynamic volume of the alginate fibres was detected regardless the structuring approach. On their exposure to physiological intragastric conditions (pH = 2), SA stabilised emulsions underwent sol–gel transition achieving a ca. 3- to 4-order increase of storage modulus (at 1 Hz). In the case of ionic sheared gel structured emulsions, exposure to physiological intragastric fluids resulted in a 10-fold reduction ability of their acid structuring ability, most likely due to the dialysis of egg-box dimer conformations by monovalent cations and protons and the sterical hindering of hydrogen bonding of MM and GG sequences under acidic conditions. Using of non-physiological simulated intragastric fluids was associated with overestimated structuring performance of SA regardless its physical state

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense using various mitochondrial DNA markers on modern and/or ancient specimens. This tends to confound the identification of refugial areas and post-glacial colonization patterns in this group. In this study we used Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g. Carpathians and Balkans) across northern regions of the continent. In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach. We identified the role of ancient and temporary land-bridges in the colonization of Scandinavia and the British Isles, with a natural colonization of Ireland deemed more likely than an ancient human-mediated introduction as has previously been proposed. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not always evident from using more limited marker sets

Supplementary material 18 from: de Jong Y, Kouwenberg J, Boumans L, Hussey C, Hyam R, Nicolson N, Kirk P, Paton A, Michel E, Guiry M, Boegh P, Pedersen H, Enghoff H, von Raab-Straube E, Güntsch A, Geoffroy M, Müller A, Kohlbecker A, Berendsohn W, Appeltans W, Arvanitidis C, Vanhoorne B, Declerck J, Vandepitte L, Hernandez F, Nash R, Costello M, Ouvrard D, Bezard-Falgas P, Bourgoin T, Wetzel F, Glöckler F, Korb G, Ring C, Hagedorn G, Häuser C, Aktaç N, Asan A, Ardelean A, Borges P, Dhora D, Khachatryan H, Malicky M, Ibrahimov S, Tuzikov A, De Wever A, Moncheva S, Spassov N, Chobot K, Popov A, Boršić I, Sfenthourakis S, Kõljalg U, Uotila P, Olivier G, Dauvin J, Tarkhnishvili D, Chaladze G, Tuerkay M, Legakis A, Peregovits L, Gudmundsson G, Ólafsson E, Lysaght L, Galil B, Raimondo F, Domina G, Stoch F, Minelli A, Spungis V, Budrys E, Olenin S, Turpel A, Walisch T, Krpach V, Gambin M, Ungureanu L, Karaman G, Kleukers R, Stur E, Aagaard K, Valland N, Moen T, Bogdanowicz W, Tykarski P, Węsławski J, Kędra M, M. de Frias Martins A, Abreu A, Silva R, Medvedev S, Ryss A, Šimić S, Marhold K, Stloukal E, Tome D, Ramos M, Valdés B, Pina F, Kullander S, Telenius A, Gonseth Y, Tschudin P, Sergeyeva O, Vladymyrov V, Rizun V, Raper C, Lear D, Stoev P, Penev L, Rubio A, Backeljau T, Saarenmaa H, Ulenberg S (2015) PESI - a taxonomic backbone for Europe. Biodiversity Data Journal 3: e5848. https://doi.org/10.3897/BDJ.3.e5848

GN-EU – a names based cyberinfrastructure contributing to the Global Names Architecture developments as a necessary component of Research Data e-Infrastructures : Framework for Action in H202

Supplementary material 4 from: de Jong Y, Kouwenberg J, Boumans L, Hussey C, Hyam R, Nicolson N, Kirk P, Paton A, Michel E, Guiry M, Boegh P, Pedersen H, Enghoff H, von Raab-Straube E, Güntsch A, Geoffroy M, Müller A, Kohlbecker A, Berendsohn W, Appeltans W, Arvanitidis C, Vanhoorne B, Declerck J, Vandepitte L, Hernandez F, Nash R, Costello M, Ouvrard D, Bezard-Falgas P, Bourgoin T, Wetzel F, Glöckler F, Korb G, Ring C, Hagedorn G, Häuser C, Aktaç N, Asan A, Ardelean A, Borges P, Dhora D, Khachatryan H, Malicky M, Ibrahimov S, Tuzikov A, De Wever A, Moncheva S, Spassov N, Chobot K, Popov A, Boršić I, Sfenthourakis S, Kõljalg U, Uotila P, Olivier G, Dauvin J, Tarkhnishvili D, Chaladze G, Tuerkay M, Legakis A, Peregovits L, Gudmundsson G, Ólafsson E, Lysaght L, Galil B, Raimondo F, Domina G, Stoch F, Minelli A, Spungis V, Budrys E, Olenin S, Turpel A, Walisch T, Krpach V, Gambin M, Ungureanu L, Karaman G, Kleukers R, Stur E, Aagaard K, Valland N, Moen T, Bogdanowicz W, Tykarski P, Węsławski J, Kędra M, M. de Frias Martins A, Abreu A, Silva R, Medvedev S, Ryss A, Šimić S, Marhold K, Stloukal E, Tome D, Ramos M, Valdés B, Pina F, Kullander S, Telenius A, Gonseth Y, Tschudin P, Sergeyeva O, Vladymyrov V, Rizun V, Raper C, Lear D, Stoev P, Penev L, Rubio A, Backeljau T, Saarenmaa H, Ulenberg S (2015) PESI - a taxonomic backbone for Europe. Biodiversity Data Journal 3: e5848. https://doi.org/10.3897/BDJ.3.e5848

How to complete taxonomic gaps in the pan-­European species registers, including experts and informatics resource

Supplementary material 29 from: de Jong Y, Kouwenberg J, Boumans L, Hussey C, Hyam R, Nicolson N, Kirk P, Paton A, Michel E, Guiry M, Boegh P, Pedersen H, Enghoff H, von Raab-Straube E, Güntsch A, Geoffroy M, Müller A, Kohlbecker A, Berendsohn W, Appeltans W, Arvanitidis C, Vanhoorne B, Declerck J, Vandepitte L, Hernandez F, Nash R, Costello M, Ouvrard D, Bezard-Falgas P, Bourgoin T, Wetzel F, Glöckler F, Korb G, Ring C, Hagedorn G, Häuser C, Aktaç N, Asan A, Ardelean A, Borges P, Dhora D, Khachatryan H, Malicky M, Ibrahimov S, Tuzikov A, De Wever A, Moncheva S, Spassov N, Chobot K, Popov A, Boršić I, Sfenthourakis S, Kõljalg U, Uotila P, Olivier G, Dauvin J, Tarkhnishvili D, Chaladze G, Tuerkay M, Legakis A, Peregovits L, Gudmundsson G, Ólafsson E, Lysaght L, Galil B, Raimondo F, Domina G, Stoch F, Minelli A, Spungis V, Budrys E, Olenin S, Turpel A, Walisch T, Krpach V, Gambin M, Ungureanu L, Karaman G, Kleukers R, Stur E, Aagaard K, Valland N, Moen T, Bogdanowicz W, Tykarski P, Węsławski J, Kędra M, M. de Frias Martins A, Abreu A, Silva R, Medvedev S, Ryss A, Šimić S, Marhold K, Stloukal E, Tome D, Ramos M, Valdés B, Pina F, Kullander S, Telenius A, Gonseth Y, Tschudin P, Sergeyeva O, Vladymyrov V, Rizun V, Raper C, Lear D, Stoev P, Penev L, Rubio A, Backeljau T, Saarenmaa H, Ulenberg S (2015) PESI - a taxonomic backbone for Europe. Biodiversity Data Journal 3: e5848. https://doi.org/10.3897/BDJ.3.e5848

Also available at: http://vbrant.eu/content/d43-design-robust-service

Supplementary material 7 from: de Jong Y, Kouwenberg J, Boumans L, Hussey C, Hyam R, Nicolson N, Kirk P, Paton A, Michel E, Guiry M, Boegh P, Pedersen H, Enghoff H, von Raab-Straube E, Güntsch A, Geoffroy M, Müller A, Kohlbecker A, Berendsohn W, Appeltans W, Arvanitidis C, Vanhoorne B, Declerck J, Vandepitte L, Hernandez F, Nash R, Costello M, Ouvrard D, Bezard-Falgas P, Bourgoin T, Wetzel F, Glöckler F, Korb G, Ring C, Hagedorn G, Häuser C, Aktaç N, Asan A, Ardelean A, Borges P, Dhora D, Khachatryan H, Malicky M, Ibrahimov S, Tuzikov A, De Wever A, Moncheva S, Spassov N, Chobot K, Popov A, Boršić I, Sfenthourakis S, Kõljalg U, Uotila P, Olivier G, Dauvin J, Tarkhnishvili D, Chaladze G, Tuerkay M, Legakis A, Peregovits L, Gudmundsson G, Ólafsson E, Lysaght L, Galil B, Raimondo F, Domina G, Stoch F, Minelli A, Spungis V, Budrys E, Olenin S, Turpel A, Walisch T, Krpach V, Gambin M, Ungureanu L, Karaman G, Kleukers R, Stur E, Aagaard K, Valland N, Moen T, Bogdanowicz W, Tykarski P, Węsławski J, Kędra M, M. de Frias Martins A, Abreu A, Silva R, Medvedev S, Ryss A, Šimić S, Marhold K, Stloukal E, Tome D, Ramos M, Valdés B, Pina F, Kullander S, Telenius A, Gonseth Y, Tschudin P, Sergeyeva O, Vladymyrov V, Rizun V, Raper C, Lear D, Stoev P, Penev L, Rubio A, Backeljau T, Saarenmaa H, Ulenberg S (2015) PESI - a taxonomic backbone for Europe. Biodiversity Data Journal 3: e5848. https://doi.org/10.3897/BDJ.3.e5848

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