Lyon Laboratory

Sainte-Foy-lès-Lyon, France

Lyon Laboratory

Sainte-Foy-lès-Lyon, France
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Hendrikx P.,French Agency for Food | Gay E.,Lyon Laboratory | Chazel M.,Lyon Laboratory | Moutou F.,Maisons Alfort Laboratory for Animal Health | And 5 more authors.
Epidemiology and Infection | Year: 2011

The purpose of this study was to develop a standardized tool for the assessment of surveillance systems on zoonoses and animal diseases. We reviewed three existing methods and combined them to develop a semi-quantitative assessment tool associating their strengths and providing a standardized way to display multilevel results. We developed a set of 78 assessment criteria divided into ten sections, representing the functional parts of a surveillance system. Each criterion was given a score according to the prescription of a scoring guide. Three graphical assessment outputs were generated using a specific combination of the scores. Output 1 is a general overview through a series of pie charts synthesizing the scores of each section. Output 2 is a histogram representing the quality of eight critical control points. Output 3 is a radar chart representing the level reached by ten system attributes. This tool was applied on five surveillance networks. © Cambridge University Press 2011.

Nouvel L.-X.,National Polytechnic Institute of Toulouse | Nouvel L.-X.,French National Institute for Agricultural Research | Marenda M.S.,National Polytechnic Institute of Toulouse | Marenda M.S.,French National Institute for Agricultural Research | And 13 more authors.
Comparative Immunology, Microbiology and Infectious Diseases | Year: 2012

Mycoplasma agalactiae causes chronic infections in small ruminants and remains endemic in many regions of the world, despite intensive and costly eradication programs. In this study, the innate genomic plasticity of . M. agalactiae was exploited to design and assess a combination of molecular epidemiological tools to trace the pathogen in different geographic locations and to understand its emergence or re-emergence after eradication campaigns. For this purpose, two collections of . M. agalactiae isolates, representing European outbreaks or localized endemic disease in a single region of France, were subjected to RFLP (Restriction Fragment Length Polymorphism) analyses using two sets of DNA probes (distributed across the genome and specific for the . vpma gene locus), and a previously described VNTR (Variable Number Tandem Repeats) analysis. A combination of four genome-specific DNA probes and two VNTRs gave the highest discriminative power. Molecular typing revealed that, while isolates from diverse geographical origins fell into clearly different groups, the endemic disease repeatedly observed in the Western Pyrenees region over the past 30. years has been caused by a unique subtype of . M. agalactiae. This indicates that the re-emergence of the pathogen after seemingly successful eradication programs is not due to the importation of exotic strains, but to the persistence of local reservoirs of infection. © 2012 Elsevier Ltd.

Lemaitre C.,University of Bordeaux 1 | Lemaitre C.,French Institute for Research in Computer Science and Automation | Barre A.,University of Bordeaux 1 | Citti C.,Toulouse 1 University Capitole | And 7 more authors.
BMC Bioinformatics | Year: 2011

Background: Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to accurately estimate alignment scores and statistical significance with sequences sharing marked compositional biases.Results: We present a general and simple methodology to build matrices that are especially fitted to the compositional bias of proteins. Our approach is inspired from the one used to build the BLOSUM matrices and is based on learning substitution and amino acid frequencies on real sequences with the corresponding compositional bias. We applied it to the large scale comparison of Mollicute AT-rich genomes. The new matrix, MOLLI60, was used to predict pairwise orthology relationships, as well as homolog families among 24 Mollicute genomes. We show that this new matrix enables to better discriminate between true and false orthologs and improves the clustering of homologous proteins, with respect to the use of the classical matrix BLOSUM62.Conclusions: We show in this paper that well-fitted matrices can improve the predictions of orthologous and homologous relationships among proteins with a similar compositional bias. With the ever-increasing number of sequenced genomes, our approach could prove valuable in numerous comparative studies focusing on atypical genomes. © 2011 Lemaitre et al; licensee BioMed Central Ltd.

Baroghel-Bouny V.,University Paris Est Creteil | Thiery M.,University Paris Est Creteil | Dierkens M.,Lyon Laboratory | Wang X.,University Paris Est Creteil
Journal of Sustainable Cement-Based Materials | Year: 2016

In real structures, gradients between inner and surface zones, which depend on the mix-design, as well as on curing and environmental conditions, are critical issues for durability, in particular when the mixture incorporates supplementary cementitious material (e.g. fly ash (FA)). This paper deals with pore structure and moisture content gradients, investigated not only on concrete samples in lab conditions, but also on reinforced concrete (RC) structural elements exposed for several years to three different outdoor environments (temperate climate, tidal zone in marine environment, as well as road and cold environment) and on full-scale structures (bridges). The experimental study was launched a lot of years ago within the framework of the large-scale and long-term “BHP 2000” French national project. The various mixtures studied (28-day cylinder compressive strengths ranging from 20 to 130 MPa) include high-performance concretes (HPCs) with or without silica fume (SF), as well as normal strength FA concretes. MIP pore size distributions obtained on the RC structural elements have been compared to lab results. In addition, in order to investigate the long-term drying(-wetting) behavior of the various types of materials studied here, water vapor desorption isotherms, internal relative humidity (RH), and degree of saturation profiles have been measured, respectively, by the saturated salt solution method, RH sensors, and gamma-ray attenuation on lab samples or on cores extracted from the elements and bridges at various times. The data have been analyzed as a function of the exposure conditions and of the mix-parameters. For example, the impact of early age external drying, carbonation, as well as freezing and thawing cycles in the presence of deicing salts has been highlighted on the field data. In addition, good performance of SF-HPCs and mature FA-concretes has been pointed out in the outdoor conditions considered. © 2016 Informa UK Limited, trading as Taylor & Francis Group

Kempf I.,British Petroleum | Kempf I.,European University of Brittany | Fleury M.A.,British Petroleum | Fleury M.A.,European University of Brittany | And 8 more authors.
International Journal of Antimicrobial Agents | Year: 2013

Colistin is a cyclic decapeptide bound to a fatty acid chain. It is active against many Gram-negative bacteria by destabilising the bacterial outer membrane. Bacteria can become resistant to colistin by modification of their lipopolysaccharide, thereby reducing the affinity of polymyxins. Colistin is often administered orally in poultry and pig production to control colibacillosis. Resistant isolates are sometimes recovered from pathological cases, particularly in piglets. However, in Europe the percentage of resistance to colistin in Escherichia coli strains isolated from the digestive tract microbiota of healthy animals remains <1%. © 2013 Elsevier B.V. and the International Society of Chemotherapy.

Tardy F.,Lyon Laboratory | Gaurivaud P.,Lyon Laboratory | Manso-Silvan L.,CIRAD - Agricultural Research for Development | Thiaucourt F.,CIRAD - Agricultural Research for Development | And 4 more authors.
Preventive Veterinary Medicine | Year: 2011

Contagious bovine pleuropneumonia (CBPP) is a severe respiratory disease of cattle and buffalo caused by Mycoplasma mycoides subsp. mycoides " Small Colony" (MmmSC). The agent of CBPP has been isolated from goats in different countries including CBPP-free areas. Goats can therefore be regarded as a putative MmmSC reservoir. No diagnostic test for CBPP surveillance in goats has been proposed as yet. Furthermore, serological tests could be seriously hampered by a widespread caprine infection due to the subspecies M. mycoides subsp. capri (Mmc), which is antigenically very close to MmmSC and displays high levels of genetic variability. A competition ELISA (cELISA) is currently used to screen for CBPP in cattle at the herd level in infected areas. The aim of this study was to see if the same cELISA would be specific enough to be used to screen goats despite the potential concomitant infection with Mmc.The cELISA titers of goats from Mmc-infected and non-infected herds were comparable and negative using the accepted cutoff for bovine sera. In contrast, seroconversion was observed in goats experimentally inoculated with an Mmc strain that cross-reacted with a monoclonal antibody targeting the same epitope as that used in cELISA. The probability of such false positivity occurring under field conditions is very low since Mmc strains with such an atypical antigenic profile emerge only rarely as a result of random nucleotide variation of the epitope-coding region. In conclusion, the commercially available cELISA can be considered specific enough to be used as a primary test to monitor passage of the CBPP agent in goats, but its sensitivity in goats requires further investigation. © 2011 Elsevier B.V.

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