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related to travel in south-eastern Asia, France, June 2019.
No full textWe report two cases of multidrug-resistant Neisseria gonorrhoeae urogenital infection with ceftriaxone resistance in a heterosexual couple in south-western France who were successfully treated with a single, high dose of intramuscular ceftriaxone (1 g). Whole genome sequencing of isolate F91 identified MLST13871, NG-MAST1086, NG-STAR233. Patient history revealed the isolate F91 was most likely acquired during a trip to Cambodia and belongs to the successful multidrug-resistant FC428 Asian clone
Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data
No full textStatic in vitro digestion tests to assess allergenic risk of novel proteins - Use of a peptidomics workflow based on free softwares
No full textIntroduction
The resistance of proteins to digestion may play a role in determining their allergenic potential. In order to evaluate the digestibility of proteins, in vitro protocols seem appropriate when ethical constraints hinder in vivo studies. In our study, the ‘pepsin resistance test’, currently used by the European Food Safety Authority to assess allergenicity of proteins is compared to more physiologically relevant in vitro digestion protocols. A peptidomics workflow based on free softwares is used to identify, quantify and perform statistical analysis on the peptides produced.
Methods
Comparison of an infant, early phase adult, and late phase adult model is being applied on a panel of allergen/non-allergen proteins from animal and vegetal origin. The proteolysis rate in gastric and intestinal compartment is determined in order to detect persistent intact protein (SDS-PAGE) and hydrolysis products larger 9 amino acids (LC-MS).
All peptidomics data (NanoLC fitted to Quadrupole-Orbitrap MS) were processed with free softwares: from data conversion to peptide identification, quantification and statistical analysis.
Results
More than two thousands NanoLC-MS/MS runs were acquired during the course of this project and the number of peptides identified ranged from one to five hundred per proteins depending on their resistance to enzymatic hydrolysis. All peptides identified (X!tandempipeline software [1]) were automatically quantified (MassChroQ [2]) in all samples, regardless the fact that it was identified at this particular time of digestion. Peptide quantification results processed in the R software environment allowed the clustering of peptides based on their behavior regarding the digestion protocol used and the digestion time (0,5 to 60min). Proteins that are not pepsin resistant show slower kinetics of proteolysis for the infant model of digestion, highlighting the fact that, for this population, they may still cause undesired immune responses via sensitization in the duodenum.
Conclusions
Differences in the kinetics of proteolysis have been found across models for proteins that are not pepsin resistant. This project highlights the importance of a multi-test protocol to assess protein digestibility.
Novel Aspect
Using a full pipeline of free softwares for peptidomics data treatment, we were able to point out peptide clusters which are only abundant when more physiologically relevant models of digestion were used
Genes Encoding Teleost Fish Ligands and Associated Receptors Remained in Duplicate More Frequently than the Rest of the Genome
No full textSignaling through ligand/receptor interactions is a widespread mechanism across all living taxa. During evolution, however, there has been a diversification in multigene families and changes in their interaction patterns. Among the events that led to the creation of new genes is the whole-genome duplication, which made possible some major innovations. Teleost fishes descended from a common ancestor which underwent one such whole-genome duplication. In our study, we investigated the effect of complete genome duplication on the evolution of ligand-receptor pairs in teleosts. We selected ten teleost species and used bioinformatics programs and phylogenetic tools in order to study the evolution of the human ligands and receptors that have orthologous genes in fishes, as well as the rest of the fish genomes. We established that since the complete duplication of the fish genomes, the conservation in duplicate copy of ligand and receptor genes is higher than expected. However, the ligand/receptor pair partners did not necessarily evolve in the same way, and a lot of situations occurred in which one of the partners returned in singleton copy when the other one was maintained in duplicate. This suggests that changes in interaction partners may have taken place during the evolution of teleosts. Moreover, the fate of the ligands and receptor coding genes is partly congruent with the phylogeny of teleosts. However, some incongruences can be observed. We suggest that these incongruences are correlated to the environment
Indexation du caractère "trayon surnuméraire" pour les races caprines Saanen et Alpine
No full textCe rapport est une étude du caractère «trayon surnuméraire» et de ses homologues fonctionnels et non fonctionnels chez les races caprines laitière Saanen et Alpine. Suite au maintien d’une fréquence résiduelle de cette tare dans les élevages mais de sa bonne héritabilité, l’objectif fixé fût l’élaboration d’une indexation pour la sélection des boucs destinés au centre de testage. Cependant, face à un caractère binaire et à la présence de différents types de trayons surnuméraires, le choix du modèle d’indexation ainsi que des caractères à indexer reste incertain. Tout au long de l’étude une comparaison des modèles linéaires et binaires est faite sur un échantillon issu de la table de pointage Capgènes du 08/04/19. En amont de l’indexation, une analyse descriptive du jeu de données est effectuée afin de faire un état des lieux des caractères étudiés (TRFS, TRS et TRF), elle est suivie par la recherche de facteurs de variations qui constitueront le modèle d’environnement, 5 effets s’avéraient significatifs. Une fois le modèle fixé, une estimation des paramètres génétique est effectuée pour chacune des races (Alpine et Saanen) et à l’aide des deux modèles (Linéaire et Binaire). La faible corrélation entre les caractères TRS et TRF traduit une indépendance des deux caractères et de la nécessité de leur indexation séparée. L’indexation des caractères TRS et TRF par les deux modèles, présente un modèle linéaire beaucoup approprié surtout pour les pères possédant un minimum de 100 filles référencées.This report is a study about supernumerary teats(SNT) and its types, functional and unfunctional, in goat breeding in Alpine and Saanen breed. With a low sustainable frequency of those characters in breeding, the goal was to index them to increase the selection of billy goat before the testing center. However, with a binary character and with the different types of SNTs the indexing model is not fixed, that is why, all along this study, we compare linear and binary model thanks to a sample of scoreboard from Capgènes (April 8th, 2019). Before indexing, we have done a descriptive analysis about our dataset to show the evolution of our characters (SNT and its types) and their frequencies in Alpine and Saanen breed. After this analysis, in a first time, we have created an environment model with 5 significant effects to estimate in a second time genetics parameters of our SNT for each breed (Alpine and Saanen), by each model. The low link between functional SNT and unfunctional SNT has shown us they are independent and must be indexed separately. Finally, theindexation has described a linear model more linked between with performance than the binary model, furthermore, this linear indexation shown she was better for billy goat with more than 100 daughters than the global sample with all billy goat
Implications nutritionnelles des directives françaises sur l’offre alimentaire en restauration scolaire et place des plats protidiques
No full textLes directives françaises pour la restauration scolaire prévoient, pour chaque série de 20 repas successifs, le respect de 15 critères relatifs à la fréquence de service de certains plats. L’objectif de l’étude était d’analyser les implications, en termes de qualité nutritionnelle des séries de repas, du respect ou non-respect de ces critères fréquentiels, notamment ceux portant sur le plat protidique. Partant de 40 séries de 20 repas successifs servis dans des écoles primaires, plusieurs séries de repas ont été simulées selon le respect ou non des critères, et la qualité nutritionnelle a été estimée par l’adéquation nutritionnelle moyenne (ANM) en 23 nutriments « positifs », ainsi que par les teneurs en lipides, acides gras saturés (AGS) et sucres libres. Les séries observées respectaient en moyenne 9,7 critères fréquentiels (min 4, max 14). Dans les séries simulées, l’ANM augmentait avec le respect des critères et diminuait suite au retrait du plat protidique ou à son remplacement par des plats sans viande ni poisson. Quel que soit le scénario, les teneurs en sucres libres étaient inférieures au maximum recommandé. Concernant les lipides et les AGS, ils diminuaient suite au respect des 15 critères ou au retrait du plat protidique, mais les teneurs les plus élevées étaient atteintes suite au remplacement du plat protidique par des plats sans viande ni poisson. Cette étude met en évidence l’intérêt nutritionnel des critères fréquentiels, et souligne la nécessité de définir la composition et la fréquence de service des plats sans viande ni poisson.The French guidelines for school meals provide for a series of 20 consecutive meals the compliance of 15 criteria related to the frequency of service of certain dishes. The objective of this study was to estimate how compliance or non-compliance with these criteria, particularly those relating to the protein dish, affects overall nutritional quality. Starting from 40 series of 20 consecutive meals served in primary schools, several series were simulated according to the compliance or non-compliance with frequency criteria, and nutritional quality was estimated by mean adequacy ratio (MAR) for 23 “positive” nutrients, as well by the content of fats, saturated fatty acids (SFA) and free sugars. The series observed respected on average 9.7 frequency criteria (min 4, max 14). In the simulated series, the MAR increased with the respect of the criteria and decreased when meat or fish-based dishes were removed or replaced by dishes without meat or fish withdrawal of the protein dish or its replacement by dishes without meat or fish. Whatever the scenario, free sugars were below the recommended maximum. Fats and SFA decreased as a result of meeting the 15 criteria; they also decreased following the withdrawal of the protein dish, but the highest levels were reached following replacement by dishes without meat or fish. This study shows the nutritional benefits of the frequency criteria, and highlights the need to define the composition of dishes without meat or fish and their frequency of service to children
Effects of reclamation effort on the recovery of ecosystem functions of a tropical degraded serpentinite dump site
No full textSurface mining or other disturbing operations on ultramafic outcrops degrade soil conditions and decrease major ecosystem functions in those habitats. Human disturbances exacerbate the harsh conditions of some ultramafic soils, making recovery more difficult. Recovery of ecosystem functions of disturbed areas may vary from passive to active reclamation measures, depending on the starting situation, available resources and expected outcomes. In this study, three treatments (topsoil application, topsoil + non-compacted, and topsoil + non-compacted + organic amendment), representing a gradient of increasing reclamation effort, were tested for the reclamation of a tropical ultramafic Spolic Technosol in Sabah (Malaysia). Soil treatments were tested at the mesocosm-scale for 12 months, and drainage water fluxes, evolution of soil physicochemical parameters, soil microbial activities and spontaneous plant colonisation, diversity and growth were monitored along the duration of the experiment. The results show that application of topsoil improved the plant biomass and water filtration functions in the non-reclaimed sites, with no additional benefit from lesser compaction. The most intensive treatment (topsoil + non-compacted + organic amendment) gave the best improvements in nutrient cycling and biomass production functions, but with a reduction of water filtration function, due to an increase in soluble concentrations and cumulative fluxes of nickel. Introduced species were dominant in the vegetation colonising the mesocosms, and therefore planting of selected native species will be necessary to create habitats for native biodiversity. This information will be useful to select a strategy for the recovery of degraded tropical serpentinite quarries and dump sites
Market Heterogeneity and the Distributional Incidence of the Soda Tax
No full textMarket heterogeneity may affect the distributional incidence of soft-drink taxes if households sort
by income across markets with different characteristics. We use the Kantar Worldpanel homescan
data to analyse the distributional incidence of the 2012 French soda tax on Exact Price Indices (EPIs)
that measure consumer welfare from the price, availability and consumption of Sugar-Sweetened
Beverages (SSBs) at a local market level. After correcting prices for consumer heterogeneity in
preferences, we find that the soda tax had a significant but small national average impact corres-
ponding to a pass-through of approximately 40%. Producers and retailers set significantly higher
pass-throughs in low-income, less-competitive and smaller markets and for cheaper but less popular
brands. Market heterogeneity ultimately has substantial distributional effects, as it accounts for
approximately 35% of the difference in welfare variation between low- and high-income consumers
