Evaluation of the presence of the bap gene in Staphylococcus aureus isolates recovered from human and animals species.

International audienceThe implication of biofilm in chronic bacterial infection in many species has triggered an increasing interest in the characterization of genes involved in biofilm formation. The bap gene is a newly identified gene that encodes the biofilm-associated protein, BAP, which is involved in biofilm formation in Staphylococcus aureus. So far the bap gene has only been found in a small proportion of S. aureus strains from bovine mastitis in Spain. In order to study the presence of the bap gene in S. aureus isolates obtained from other species and various locations, a collection of 262 isolates was tested by PCR, using published primers and dot-blot. The results indicated that none of the isolates carried the bap gene suggesting that the prevalence of this gene among S. aureus isolates should be very low

Report on the First Detection of Pectenotoxin-2, Spirolide-A and Their Derivatives in French Shellfish

In the context of the French Phytoplankton and Phycotoxins Monitoring Network (REPHY) programme, shellfish samples were harvested from different locations where harmful algae blooms were known to have occurred. For all shellfish samples found positive by the mouse bioassay for diarrhetic shellfish poisoning (DSP) toxins, liquid chromatography (LC) coupled with mass spectrometry (MS) was used to search for the following lipophilic toxins: okadaic acid (OA), dinophysistoxins (DTXs), pectenotoxins (PTXs), azaspiracids (AZAs), yessotoxins (YTXs), spirolides (SPXs) and gymnodimines (GYMs). In order to investigate the presence of acyl-OAs and/or acyl-DTX-1,-2 (DTX-3), alkaline hydrolysis was performed on all samples, and LC/MS analyses were carried out on the samples before and after hydrolysis. The results revealed different lipophilic toxin profiles as a function of the shellfish sampling location. The primary finding was that all of the samples contained OA and acyl-OA. In addition, other lipophilic toxins were found in shellfish samples: DTX-2, acyl-DTX-2 and SPXs (SPX-A, SPX-desMeC) on the Atlantic coast (Southern Brittany, Arcachon), and pectenotoxins (PTX-2, PTX-2-seco-acid and 7-epi-PTX-2-seco-acid) on the Mediterranean coast (Thau lagoon, the island of Corsica). This paper reports on the first detection of PTX-2, SPX-A and their derivatives in French shellfish

ATONTE: towards a new methodology for seed ontology development from texts and experts

Publication déjà téléversée dans HAL sous la référéence hal-03954342ATONTE (ATlantis methodology for ONtology development from Texts and Experts) is a methodology for the manual development of low-level seed ontologies. The modelling process is based on a combination of knowledge from non-fiction text corpora such as manuals, information guides or sets of instructions, and the knowledge of domain experts. This article presents the five key steps of the ATONTE process. Seed ontologies created with ATONTE can be used to develop and populate knowledge graphs for use in specific applications within given technical domains

ATLANTIS : Une ontologie pour représenter les Instructions nautiques

La publication a déjà été téléversée dans HAL sous la référence https://hal.science/hal-03695242v2Les Instructions nautiques sont une série d’ouvrages produits et publiés par le Service hydrographique et océanographique de la Marine (Shom) qui donnent aux navigateurs les informations nécessaires pour naviguer près des côtes et accéder aux ports. Dans cet article, nous présentons l’ontologie ATLANTIS (coAsTaL mAritime NavigaTion InstructionS) que nous avons développée pour modéliser les connaissances contenues dans ces ouvrages, ainsi qu’un retour d’expérience et des adaptations que nous avons apportées à la Simplified Agile Methodology for Ontology Development (SAMOD), la méthodologie de développement d’ontologies que nous avons employée

Analyses linguistiques et techniques d'alignement pour créer et enrichir une ontologie topographique

National audienceOne of the goals of the GéOnto project is to build an ontology of topographic concepts. This ontology results from the enrichment of a first taxonomy developed beforehand, through the analysis of two types of textual documents: technical database specifications and description of journeys. This work relies on natural language processing and ontology alignment techniques, as well as external knowledge resources such as dictionaries and gazetteers.Dans cet article, nous présentons le projet GéOnto dont un des buts est de construire une ontologie de concepts topographiques. Cette ontologie est réalisée par enrichissement d'une première taxonomie de termes réalisée précédemment, et ce grâce à l'analyse de deux types de documents textuels : des spécifications techniques de bases de données et des récits de voyage. Cet enrichissement s'appuie sur des techniques automatiques de traitement du langage et d'alignement d'ontologies, ainsi que sur des connaissances externes comme des dictionnaires et des bases de toponymes

Radiographic assessment of the femorotibial joint of the CCLT rabbit experimental model of osteoarthritis

<p>Abstract</p> <p>Background</p> <p>The purposes of the study were to determine the relevance and validity of in vivo non-invasive radiographic assessment of the CCLT (Cranial Cruciate Ligament Transection) rabbit model of osteoarthritis (OA) and to estimate the pertinence, reliability and reproducibility of a radiographic OA (ROA) grading scale and associated radiographic atlas.</p> <p>Methods</p> <p>In vivo non-invasive extended non weight-bearing radiography of the rabbit femorotibial joint was standardized. Two hundred and fifty radiographs from control and CCLT rabbits up to five months after surgery were reviewed by three readers. They subsequently constructed an original semi-quantitative grading scale as well as an illustrative atlas of individual ROA feature for the medial compartment. To measure agreements, five readers independently scored the same radiographic sample using this atlas and three of them performed a second reading. To evaluate the pertinence of the ROA grading scale, ROA results were compared with gross examination in forty operated and ten control rabbits.</p> <p>Results</p> <p>Radiographic osteophytes of medial femoral condyles and medial tibial condyles were scored on a four point scale and dichotomously for osteophytes of medial fabella. Medial joint space width was scored as normal, reduced or absent. Each ROA features was well correlated with gross examination (p < 0.001). ICCs of each ROA features demonstrated excellent agreement between readers and within reading. Global ROA score gave the highest ICCs value for between (ICC 0.93; CI 0.90-0.96) and within (ICC ranged from 0.94 to 0.96) observer agreements. Among all individual ROA features, medial joint space width scoring gave the highest overall reliability and reproducibility and was correlated with both meniscal and cartilage macroscopic lesions (r_s= 0.68 and r_s= 0.58, p < 0.001 respectively). Radiographic osteophytes of the medial femoral condyle gave the lowest agreements while being well correlated with the macroscopic osteophytes (r_s= 0.64, p < 0.001).</p> <p>Conclusion</p> <p>Non-invasive in vivo radiography of the rabbit femorotibial joint is feasible, relevant and allows a reproducible grading of experimentally induced OA lesion. The radiographic grading scale and atlas presented could be used as a template for in vivo non invasive grading of ROA in preclinical studies and could allow future comparisons between studies.</p

Beyond the water column: aquatic hyphomycetes outside their preferred habitat

Aquatic hyphomycetes have adapted to running waters by their uncommon conidial shape, which facilitates dispersal as well as adherence to plant substrata. However, they have been early and regularly reported to occur in a variety of environments other than their preferred habitat (e.g., in lentic freshwaters, brackish and marine environments, in terrestrial niches such as stream banks, dew, canopy waters and tree holes). In addition, several aquatic hyphomycetes have adapted to a mutualistic lifestyle which may involve plant defence, as endophytes in leaves, gymnosperm needles, orchids and terrestrial roots. There are several lines of evidence suggesting that aquatic hyphomycetes survive under terrestrial conditions due to their sexual states. Although exhibiting higher diversity in pristine streams, aquatic hyphomycetes can survive environmental stress, e.g., pollution or river intermittency. They also inhabit ground and hyporheic waters, where they appear to be subjected to both physical and physiological selection. Appropriate methods including molecular ones should provide a more comprehensive view of the occurrence and ecological roles of aquatic hyphomycetes outside their preferred habitat