Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels

The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica

Performance assessment of ontology matching systems for FAIR data

© The Author(s). 2022 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.Background: Ontology matching should contribute to the interoperability aspect of FAIR data (Findable, Accessible, Interoperable, and Reusable). Multiple data sources can use different ontologies for annotating their data and, thus, creating the need for dynamic ontology matching services. In this experimental study, we assessed the performance of ontology matching systems in the context of a real-life application from the rare disease domain. Additionally, we present a method for analyzing top-level classes to improve precision. Results: We included three ontologies (NCIt, SNOMED CT, ORDO) and three matching systems (AgreementMakerLight 2.0, FCA-Map, LogMap 2.0). We evaluated the performance of the matching systems against reference alignments from BioPortal and the Unified Medical Language System Metathesaurus (UMLS). Then, we analyzed the top-level ancestors of matched classes, to detect incorrect mappings without consulting a reference alignment. To detect such incorrect mappings, we manually matched semantically equivalent top-level classes of ontology pairs. AgreementMakerLight 2.0, FCA-Map, and LogMap 2.0 had F1-scores of 0.55, 0.46, 0.55 for BioPortal and 0.66, 0.53, 0.58 for the UMLS respectively. Using vote-based consensus alignments increased performance across the board. Evaluation with manually created top-level hierarchy mappings revealed that on average 90% of the mappings’ classes belonged to top-level classes that matched. Conclusions: Our findings show that the included ontology matching systems automatically produced mappings that were modestly accurate according to our evaluation. The hierarchical analysis of mappings seems promising when no reference alignments are available. All in all, the systems show potential to be implemented as part of an ontology matching service for querying FAIR data. Future research should focus on developing methods for the evaluation of mappings used in such mapping services, leading to their implementation in a FAIR data ecosystem

Etude de la germination de cinq provenances de Tamarindusindica L. en conditions de stress hydrique au Sénégal

Ce présent travail se propose d’évaluer le comportement germinatif de cinq provenances de tamarinier (Tamarindus indica L.) dans des conditions de stress  hydrique. Six concentrations croissantes 0 ; - 1,4 ; - 2,8 ; - 4,2 ; - 5,6 ; -7 bar de polyéthylène glycol (PEG 6000) ont été testées. Les résultats ont montré une  variabilité de la germination de l’espèce en fonction de l’intensité du stress et de la provenance. Le seuil critique de germination des provenances du tamarinier est  de -7 bar. La provenance Sakkal de la zone sahélienne s’est montrée plus tolérante au stress hydrique avec un taux de germination de 2% en conditions de stress  sévère. Toutefois, ces faibles résultats sont imputables aux conditions de conservation des graines. Ces informations sur l'écologie et la physiologie de la  germination du tamarinier sont vitales, non seulement pour comprendre les variations génétiques des différentes populations de tamarinier au Sénégal, mais aussi pour développer des stratégies pour la conservation de la biodiversité et la restauration des forêts tropicales.Mots clés : Germination, provenances, Tamarindus indica L., stress hydrique, Sénégal

Occurrence, distribution and diversity of Listeria monocytogenes contamination on beef and pig carcasses after slaughter

In this study we investigated the prevalence and location of Listeria monocytogenes and hygiene indicator bacteria on beef and pig carcasses. Carcasses were sampled after slaughter and before cooling at eight and nine sites on the carcass, respectively. For each sample, detection and enumeration of Listeria was performed, as well as the enumeration of Total Aerobic Counts (TAC) and Enterobacteriaceae. The L. monocytogenes isolates were also typed to determine pulsotypes and clonal complexes (CC). L. monocytogenes was detected on 46% [95% CI: 35-56%] of beef and 22% [95% CI: 11-32%] of pig carcasses. Contamination levels at the different carcass sites differed considerably between beef and pigs. Genetic typing of strains suggests that carcass contamination originates from both incoming animals with transmission during slaughter practices as well as persistent (CC9) contamination from the slaughterhouse environment. These findings can be used to understand the complexity of introduction and persistence of this pathogen in slaughter facilities. Accurate correlation of L. monocytogenes presence proved unfeasible with any of the tested hygiene indicator bacteria

A Solution to Weed Control in Grassland Containing White Clover

Productive grass with white clover can lead to advantages both in forage quantity and quality, economics and in meeting wider expectations detailed in recent EU and UK policy. The ability to achieve this agronomic success is currently difficult due to a lack of options for broad spectrum weed control that also allow establishment or preservation of a white clover population. The aim of this paper is to demonstrate that 3730XL, developed by Corteva Agriscience, is a solution to this critical success factor. Data is presented from 16 efficacy trials (10 from established grassland and 5 from newly sown) where white clover cover of plots treated with 3730XL was recorded relative to an untreated plot. Data is also presented from 106 weed control trials, against a selection of species, demonstrating the efficacy of 3730XL split by grassland scenario. The evidence presented highlights the capability of 3730XL to both control a broad spectrum of weed species and allow the establishment or preservation of white clover. Consequently, growers are able to cultivate the associated benefits that this confers

Protein processing characterized by a gel-free proteomics approach

We describe a method for the specific isolation of representative N-terminal peptides of proteins and their proteolytic fragments. Their isolation is based on a gel-free, peptidecentric proteomics approach using the principle of diagonal chromatography. We will indicate that the introduction of an altered chemical property to internal peptides holding a free α-N-terminus results in altered column retention of these peptides, thereby enabling the isolation and further characterization by mass spectrometry of N-terminal peptides. Besides pointing to changes in protein expression levels when performing such proteome surveys in a differential modus, protease specificity and substrate repertoires can be allocated since both are specified by neo-N-termini generated after a protease cleavage event. As such, our gel-free proteomics technology is widely applicable and amenable for a variety of proteome-driven protease degradomics research

Effectiveness of rotavirus vaccination in prevention of hospital admissions for rotavirus gastroenteritis among young children in Belgium : case-control study

Objective : To evaluate the effectiveness of rotavirus vaccination among young children in Belgium. Design : Prospective case-control study. Setting : Random sample of 39 Belgian hospitals, February 2008 to June 2010. Participants : 215 children admitted to hospital with rotavirus gastroenteritis confirmed by polymerase chain reaction and 276 age and hospital matched controls. All children were of an eligible age to have received rotavirus vaccination (that is, born after 1 October 2006 and aged >= 14 weeks). Main outcome measure : Vaccination status of children admitted to hospital with rotavirus gastroenteritis and matched controls. Results : 99 children (48%) admitted with rotavirus gastroenteritis and 244 (91%) controls had received at least one dose of any rotavirus vaccine (P= 12 months. The G2P[4] genotype accounted for 52% of cases confirmed by polymerase chain reaction with eligible matched controls. Vaccine effectiveness was 85% (64% to 94%) against G2P[4] and 95% (78% to 99%) against G1P[8]. In 25% of cases confirmed by polymerase chain reaction with eligible matched controls, there was reported co-infection with adenovirus, astrovirus and/or norovirus. Vaccine effectiveness against co-infected cases was 86% (52% to 96%). Effectiveness of at least one dose of any rotavirus vaccine (intention to vaccinate analysis) was 91% (82% to 95%). Conclusions : Rotavirus vaccination is effective for the prevention of admission to hospital for rotavirus gastroenteritis among young children in Belgium, despite the high prevalence of G2P[4] and viral co-infection