Contrôle de la contamination de Listeria monocytogenes dans les drains d'industries alimentaires

L’innocuité microbiologique des surfaces a toujours été d’importance capitale en industrie agroalimentaire. Bien que ce point soit connu de tous, les moyens de lutte sont en constante évolution grâce à la compréhension et à la maîtrise de l‘adhésion, de la croissance et de la dispersion des microorganismes, afin de lutter contre la propagation et la multiplication de microorganismes pathogènes dans de ce type d’industrie. Dans cette étude, on a cherché à confronter un organisme pathogène alimentaire connu, Listeria monocytogenes, à un produit commercial composé d’une matrice détergente classique et d’un consortium bactérien de plusieurs souches de Bacillus sélectionnées par notre partenaire industriel en vue de se rapprocher le plus de la réalité des drains en industrie agroalimentaire. Les études ont été réalisées aux températures de 10, 20 et 30°C, dans un système avec ou sans agitation, dans un milieu riche en nutriments (Infusion cœur cervelle en anglais Brain Heart Infusion) afin que les nutriments ne soient pas une limite à la croissance. Deux concentrations ont été utilisées dans cette étude, pour l’organisme pathogène (3 et 5 log ufc/mL) et pour le produit commercial (consortium bactérien à 3 et 5 log ufc/mL). Des courbes de croissance en culture pure et en conditions compétitives ont été effectuées afin de comparer l’effet du produit commercial sur L. monocytogenes. Un suivi du pH est également réalisé afin d’analyser l’activité microbiologique dans le millieu. On observe que globalement, le produit a la capacité d’inhiber le microorganisme pathogène de plus d’1 log d’ufc/mL. De plus, l’inhibition est favorisée à 10°C lorsque le consortium bactérien est à 5 log ufc/mL et lorsque L. monocytogenes est à 3 log ufc/mL. L’agitation a également un effet positif en amplifiant l’inhibition de l’organisme pathogène en favorisant la croissance de la flore compétitive du produit commercial composée essentiellement de microorganismes aérobiques. C’est pour cela que la plus grande efficacité de la méthode est à 10°C en agitation pour la compétition consortium bactérien (avec matrice) à 5 log ufc/mL et L. monocytogenes à 3 log ufc/mL. Cet effet pourrait être en partie dû à la matrice détergente qui compose le produit. A 10°C : la première compétition est le consortium à 5 log ufc/mL-L. monocytogenese à 5 log ufc/mL, le microorganisme pathogène perd 1 log ufc/mL par rapport aux 5 log d’origine. Le deuxième est le consortium à 5 log ufc/mL- L. monocytogenese à 3 log ufc/mL, dans ce cas il diminue jusqu'à passer sous le seuil de détection; une différence de 9 log ufc/mL sépare le dénombrement la culture pure de L. monocytogenes par rapport à la culture en compétition dans les mêmes conditions. Alors qu’à 10°C en compétition avec L. monocytogenes à 3 et 5 log ufc/mL, lorsque le consortium bactérien est à 3 log ufc/mL cette fois-ci, aucune modification de la croissance de L. monocytogenes n’est observée par rapport à sa croissance en culture pure, que ce soit avec ou sans agitation. Ce système est complexe, les phénomènes contrôlant la croissance de ces bactéries dans le milieu sont multiples et agissent en synergie. Le présent document se propose de détailler ces interactions entre les bactéries qui se compétitionnent et la matrice détergente du produit.The microbiological cleanliness of surfaces has always been of paramount importance in the food industry. Although this is known to all, means of ensuring this are constantly improving due to a better understanding of bacterial adhesion, growth and spread, to fight against the propagation and growthing pathogenic microorganisms in this type of industry. A known foodborne pathogen: Listeria monocytogenes was exposed to a commercial product composed of a conventional detergent matrix and a bacterial consortium of several strains of Bacillus selected by our industrial partner seeking to be close to real drain conditions in industrial food processing plants. The experiments are performed at 10, 20 and 30°C, in a system with or without agitation and in an environment rich in nutrients (Brain Heart Infusion) to avoid cell growth restriction. Two concentrations were used in this study for the pathogen (3 and 5 log cfu/mL) and the commercial product (bacterial consortium at 3 and 5 log cfu/mL). Growth curves of pure culture and culture in competition were produced in order to compare the effect of the commercial product on the pathogen. pH monitoring is also carried out to analyze the microbiological activity in the environment. It was observed that the commercial product is able to inhibit the pathogen. Overall, this inhibition is stronger at 30, than at 10 °C. In addition, the inhibition is favored when the bacterial consortium is at 5 log cfu/mL and when L. monocytogenes is at 3 log cfu/mL. Agitation also has a positive effect by amplifying the inhibition of the pathogen by promoting the growth of competitive flora of the commercial product consisting mainly of aerobic microorganisms. The greatest efficacy is observed at 10 °C with stirring for two competitions, probably because of the inhibitory effect of the matrix itself. The first competition was when the consortium was at 5 log cfu/mL - pathogen log 5 cfu/mL: pathogen cell counts were reduced by 1 log cfu/mL with an initial 5 log cfu/mL at the beginning. The second concentration was with the consortium at 5 log cfu/mL – pathogen 3 log cfu/mL. In this case, L. monocytogenes decrease to go under the detection limit, a difference of 9 log cfu/mL between the pure culture and culture in competition. However, at 10°C in competition, when the bacterial consortium was at 3 log cfu/mL, no change was observed in the growth of L. monocytogenes in relation to its growth in pure culture, whether with or without agitation. This system is complex. Phenomena controlling the growth of these bacteria in the environment are multiple and may act synergistically. This document provides details of these interactions with the competing bacteria and the product’s matrix

Etude de la fonction cardiaque 4D à partir de ciné cardiaque 3D via une synchronisation sur la respiration et rythme cardiaque: travail de Bachelor

Objectifs : Dans le cadre de l’exploration cardiaque en IRM, nous expérimentons une séquence 4D à partir d’une séquence 4D Flow. L’objectif est de calculer la fraction d’éjection et de la comparer avec la séquence 2D ciné (gold standard actuel) utilisée cliniquement. Grâce à des outils statistiques, nous évaluons la reproductibilité intra- et inter-opérateurs de la séquence 4D. Nous regardons également la précision de cette séquence en comparant les résultats des segmentations 4D aux segmentations de la séquence 2D ciné. Méthodologie : Dans un premier temps, nous avons optimisé la séquence 4D en modifiant certains paramètres comme la vitesse d’encodage retenue à 30cm/s et le tracking factor (tf) de 0.6 × mouvement mesuré (au niveau du diaphragme). Les séquences ont été réalisées, à quatre temps différents, sur trois individus sains. Dans un second temps, nous avons calculé la fraction d’éjection du ventricule gauche (FEVG) en le segmentant en diastole et en systole selon la méthode Simpson. Cela a été fait sur la séquence 4D et sur la 2D ciné, deux fois, afin d’obtenir des données plus conséquentes pour mesurer la corrélation entre les deux techniques et la variabilité entre chaque opérateur. Enfin, chaque valeur obtenue est introduite dans un tableau Excel, puis convertie sous forme d’équation ICC et Bland-Altman. A partir de ça, nous calculons la variabilité intra- et inter-opérateur, ce qui nous permet de visualiser la concordance de nos résultats et de comparer les valeurs obtenues pour le 4D avec celles obtenues pour le 2D ciné. Résultats : Les calculs ICC donnent des valeurs entre 0.71 et 0.96 pour les différents temps d'acquisitions. Ces données traduisent de bonnes corrélation et reproductibilité intra-opérateur, par rapport à ce que dit la littérature (> 0.75). Quant à la variabilité inter-opérateur, elle est, dans l'ensemble, en dessous de la valeur de référence (< 0.4) synonyme d'une faible corrélation entre opérateur. Suite à ces résultats peu encourageants, nous voulions trouver la source d’erreur. En étudiant les volumes systoliques et diastoliques séparément (et non la FEVG), nous constatons un résultat élevé en diastole (0.78), mais en dessous de nos moyennes en systole (0.4). Conclusion : Suite à l'analyse de nos résultats, nous constatons que le travail de segmentation de chacun d'entre nous subit une amélioration avec le temps et nous permet de diminuer la variabilité entre 2D ciné et 4D. La reproductibilité est observée en intra- mais est à réévaluer de façon plus approfondie en inter-opérateur

Gene flow and genetic divergence among mainland and insular populations across the south-western range of the Eurasian treecreeper (Certhia familiaris , Aves)

International audienceThe Eurasian treecreeper (Certhia familiaris) comprises two mitochondrial lineages that diverged during the mid-Pleistocene. One palaeoendemic lineage has an allopatric range currently restricted to the island of Corsica and the Caucasus region, whereas the second one has a very large Eurasian range. Here, we used microsatellites (N = 6) and mitochondrial DNA (COI) to assess the genetic structure of insular and mainland populations from Corsica, mainland France and Central Italy (N = 258) and the level of mitochondrial and nuclear gene flow among these populations. Concordant with the mitochondrial DNA signal, the results for microsatellites clearly demonstrate that the Corsican population (Certhia familiaris corsa) is strongly divergent from nearby mainland populations (Certhia familiaris macrodactyla). Microsatellite data also support significant divergence and low gene flow between the Central Italian and mainland French populations. Our results suggest low nuclear gene flow from the mainland into Corsica and no mitochondrial gene flow. Sporadic gene flow from the nearby mainland might explain the presence of continental nuclear alleles in the genome of 5% of sampled insular birds. Our study confirms the existence of an endemic Corsican treecreeper lineage with important conservation value. Our results also imply that Eurasian treecreepers from Central Italy constitute a distinct management unit

Tracing the colonization history of the Indian Ocean scops-owls (Strigiformes: Otus) with further insight into the spatio-temporal origin of the Malagasy avifauna

<p>Abstract</p> <p>Background</p> <p>The island of Madagascar and surrounding volcanic and coralline islands are considered to form a biodiversity hotspot with large numbers of unique taxa. The origin of this endemic fauna can be explained by two different factors: vicariance or over-water-dispersal. Deciphering which factor explains the current distributional pattern of a given taxonomic group requires robust phylogenies as well as estimates of divergence times. The lineage of Indian Ocean scops-owls (<it>Otus</it>: Strigidae) includes six or seven species that are endemic to Madagascar and portions of the Comoros and Seychelles archipelagos; little is known about the species limits, biogeographic affinities and relationships to each other. In the present study, using DNA sequence data gathered from six loci, we examine the biogeographic history of the Indian Ocean scops-owls. We also compare the pattern and timing of colonization of the Indian Ocean islands by scops-owls with divergence times already proposed for other bird taxa.</p> <p>Results</p> <p>Our analyses revealed that Indian Ocean islands scops-owls do not form a monophyletic assemblage: the Seychelles <it>Otus insularis </it>is genetically closer to the South-East Asian endemic <it>O. sunia </it>than to species from the Comoros and Madagascar. The Pemba Scops-owls <it>O. pembaensis</it>, often considered closely related to, if not conspecific with <it>O. rutilus </it>of Madagascar, is instead closely related to the African mainland <it>O. senegalensis</it>. Relationships among the Indian Ocean taxa from the Comoros and Madagascar are unresolved, despite the analysis of over 4000 bp, suggesting a diversification burst after the initial colonization event. We also highlight one case of putative back-colonization to the Asian mainland from an island ancestor (<it>O. sunia</it>). Our divergence date estimates, using a Bayesian relaxed clock method, suggest that all these events occurred during the last 3.6 myr; albeit colonization of the Indian Ocean islands were not synchronous, <it>O. pembaensis </it>diverged from <it>O. senegalensis </it>about 1.7 mya while species from Madagascar and the Comoro diverged from their continental sister-group about 3.6 mya. We highlight that our estimates coincide with estimates of diversification from other bird lineages.</p> <p>Conclusion</p> <p>Our analyses revealed the occurrence of multiple synchronous colonization events of the Indian Ocean islands by scops-owls, at a time when faunistic exchanges involving Madagascar was common as a result of lowered sea-level that would have allowed the formation of stepping-stone islands. Patterns of diversification that emerged from the scops-owls data are: 1) a star-like pattern concerning the order of colonization of the Indian Ocean islands and 2) the high genetic distinctiveness among all Indian Ocean taxa, reinforcing their recognition as distinct species.</p

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

Abstract: Background: Birds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day and owls (Strigiformes) hunting by night. Results: Here, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identify common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems, such as loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems that are convergent with other nocturnal avian orders. Additionally, we find that a suite of genes associated with vision and circadian rhythm are differentially expressed in blood tissue between nocturnal and diurnal raptors, possibly indicating adaptive expression change during the transition to nocturnality. Conclusions: Overall, raptor genomes show genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes

We report here the assembly of a northern spotted owl (Strix occidentalis caurina) genome. We generated Illumina paired-end sequence data at 90× coverage using nine libraries with insert lengths ranging from ∼250 to 9,600 nt and read lengths from 100 to 375 nt. The genome assembly is comprised of 8,108 scaffolds totaling 1.26 × 109 nt in length with an N50 length of 3.98 × 106 nt. We calculated the genome-wide fixation index (FST) of S. o. caurina with the closely related barred owl (Strix varia) as 0.819. We examined 19 genes that encode proteins with light-dependent functions in our genome assembly as well as in that of the barn owl (Tyto alba). We present genomic evidence for loss of three of these in S. o. caurina and four in T. alba. We suggest that most light-associated gene functions have been maintained in owls and their loss has not proceeded to the same extent as in other dim-light-adapted vertebrates

Evidence for a Rad18-Independent Frameshift Mutagenesis Pathway in Human Cell-Free Extracts

Bypass of replication blocks by specialized DNA polymerases is crucial for cell survival but may promote mutagenesis and genome instability. To gain insight into mutagenic sub-pathways that coexist in mammalian cells, we examined N-2-acetylaminofluorene (AAF)-induced frameshift mutagenesis by means of SV40-based shuttle vectors containing a single adduct. We found that in mammalian cells, as previously observed in E. coli, modification of the third guanine of two target sequences, 5'-GGG-3' (3G) and 5'-GGCGCC-3' (NarI site), induces –1 and –2 frameshift mutations, respectively. Using an in vitro assay for translesion synthesis, we investigated the biochemical control of these events. We showed that Pol eta, but neither Pol iota nor Pol zeta, plays a major role in the frameshift bypass of the AAF adduct located in the 3G sequence. By complementing PCNA-depleted extracts with either a wild-type or a non-ubiquitinatable form of PCNA, we found that this Pol eta-mediated pathway requires Rad18 and ubiquitination of PCNA. In contrast, when the AAF adduct is located within the NarI site, TLS is only partially dependent upon Pol eta and Rad18, unravelling the existence of alternative pathways that concurrently bypass this lesion

Role of the ubiquitin-binding domain of Polη in Rad18-independent translesion DNA synthesis in human cell extracts

In eukaryotic cells, the Rad6/Rad18-dependent monoubiquitination of the proliferating cell nuclear antigen (PCNA) plays an essential role in the switching between replication and translesion DNA synthesis (TLS). The DNA polymerase Polη binds to PCNA via a consensus C-terminal PCNA-interacting protein (PIP) motif. It also specifically interacts with monoubiquitinated PCNA thanks to a recently identified ubiquitin-binding domain (UBZ). To investigate whether the TLS activity of Polη is always coupled to PCNA monoubiquitination, we monitor the ability of cell-free extracts to perform DNA synthesis across different types of lesions. We observe that a cis-syn cyclobutane thymine dimer (TT-CPD), but not a N-2-acetylaminofluorene-guanine (G-AAF) adduct, is efficiently bypassed in extracts from Rad18-deficient cells, thus demonstrating the existence of a Polη-dependent and Rad18-independent TLS pathway. In addition, by complementing Polη-deficient cells with PIP and UBZ mutants, we show that each of these domains contributes to Polη activity. The finding that the bypass of a CPD lesion in vitro does not require Ub-PCNA but nevertheless depends on the UBZ domain of Polη, reveals that this domain may play a novel role in the TLS process that is not related to the monoubiquitination status of PCNA

Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa

<p>Abstract</p> <p>Background</p> <p>The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (<it>Phyllastephus debilis</it>) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies <it>albigula </it>(green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies <it>rabai </it>(grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (<it>Phyllastrephus debilis</it>) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages.</p> <p>Results</p> <p>We found significant biometric differences between the lowland (<it>rabai</it>) and montane (<it>albigula</it>) populations in Tanzania. The differences in shape are coupled with discrete differences in the coloration of the underparts. Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages. The divergence between the two forms occurred between 2.4 and 3.1 Myrs ago.</p> <p>Our coalescent analyses suggest that limited gene flow, mostly from the subspecies <it>rabai </it>to <it>albigula</it>, is taking place at three mid-altitude localities, where lowland and montane rainforest directly abut. The extent of this introgression appears to be limited and is likely a consequence of the recent expansion of <it>rabai </it>further inland.</p> <p>Conclusion</p> <p>The clear altitudinal segregation in morphology found within the Tiny Greenbul is the result of secondary contact of two highly differentiated lineages rather than disruptive selection in plumage pattern across an altitudinal gradient. Based on our results, we recommend <it>albigula </it>be elevated to species rank.</p

The ANTENATAL multicentre study to predict postnatal renal outcome in fetuses with posterior urethral valves: objectives and design

Abstract Background Posterior urethral valves (PUV) account for 17% of paediatric end-stage renal disease. A major issue in the management of PUV is prenatal prediction of postnatal renal function. Fetal ultrasound and fetal urine biochemistry are currently employed for this prediction, but clearly lack precision. We previously developed a fetal urine peptide signature that predicted in utero with high precision postnatal renal function in fetuses with PUV. We describe here the objectives and design of the prospective international multicentre ANTENATAL (multicentre validation of a fetal urine peptidome-based classifier to predict postnatal renal function in posterior urethral valves) study, set up to validate this fetal urine peptide signature. Methods Participants will be PUV pregnancies enrolled from 2017 to 2021 and followed up until 2023 in >30 European centres endorsed and supported by European reference networks for rare urological disorders (ERN eUROGEN) and rare kidney diseases (ERN ERKNet). The endpoint will be renal/patient survival at 2 years postnatally. Assuming α = 0.05, 1–β = 0.8 and a mean prevalence of severe renal outcome in PUV individuals of 0.35, 400 patients need to be enrolled to validate the previously reported sensitivity and specificity of the peptide signature. Results In this largest multicentre study of antenatally detected PUV, we anticipate bringing a novel tool to the clinic. Based on urinary peptides and potentially amended in the future with additional omics traits, this tool will be able to precisely quantify postnatal renal survival in PUV pregnancies. The main limitation of the employed approach is the need for specialized equipment. Conclusions Accurate risk assessment in the prenatal period should strongly improve the management of fetuses with PUV