Microbiological aspects of methane emission in a ricefield soil from the Camargue (France) : 2. Methanotrophy and related microflora

Les principaux facteurs qui influencent l'activité méthanotrophe du sol (épaisseur du sol, humidité, addition d'engrais et dessiccation) ont été étudiés in vitro sur un sol de rizière de Camargue (France) afin de standardiser une méthode pour estimer l'activité méthanotrophe potentielle (PMA) d'un sol. La possibilité d'énumérer les méthanotrophes du sol a été étudiée et les souches dominantes du sol incubé pendant un mois sous un mélange de 80% air/20% CH4 ont été isolées. La méthanotrophie in vitro est un phénomène quantifiable par unité de surface plutôt que par unité de poids de sol. L'activité maximale (PMA)(1.8 mole m-2 j-1) a été mesurée sur un échantillon à une humidité voisine de la capacité au champ et incubé pendant un mois sous air/CH4. Les consommations de CH4 et d'O2 ainsi que la production de CO2 sont fortement corrélées. La consommation d'O2 liée à l'activité hétérotrophe du sol est négligeable comparée à celle due à l'activité méthanotrophe. L'addition d'engrais à des concentrations utilisées en agriculture est sans effet sur la PMA qui est restée stable pendant deux ans dans le sol conservé à l'état sec. Une très forte contamination rend les étalements sur boites de Pétri inexploitables pour dénombrer les bactéries méthanotrophes du sol. Les populations estimées par MPN sont faibles dans le sol sec (2.5 x 102 g-1) et atteignent 5 x 108 g-1 dans le sol enrichi. La morphologie des souches isolées indique leur appartenance aux bactéries méthanotrophes de type II. (Résumé d'auteur

The Vitamin A Derivative All-Trans Retinoic Acid Repairs Amyloid-β-Induced Double-Strand Breaks in Neural Cells and in the Murine Neocortex.

The amyloid-β peptide or Aβ is the key player in the amyloid-cascade hypothesis of Alzheimer's disease. Aβ appears to trigger cell death but also production of double-strand breaks (DSBs) in aging and Alzheimer's disease. All-trans retinoic acid (RA), a derivative of vitamin A, was already known for its neuroprotective effects against the amyloid cascade. It diminishes, for instance, the production of Aβ peptides and their oligomerisation. In the present work we investigated the possible implication of RA receptor (RAR) in repair of Aβ-induced DSBs. We demonstrated that RA, as well as RAR agonist Am80, but not AGN 193109 antagonist, repair Aβ-induced DSBs in SH-SY5Y cells and an astrocytic cell line as well as in the murine cortical tissue of young and aged mice. The nonhomologous end joining pathway and the Ataxia Telangiectasia Mutated kinase were shown to be involved in RA-mediated DSBs repair in the SH-SY5Y cells. Our data suggest that RA, besides increasing cell viability in the cortex of young and even of aged mice, might also result in targeted DNA repair of genes important for cell or synaptic maintenance. This phenomenon would remain functional up to a point when Aβ increase and RA decrease probably lead to a pathological state

Improving mealtimes for paediatric intensive care children and families : a quality improvement initiative

Introduction: Many critically ill children can be fed orally at some point during their paediatric intensive care (PICU) stay, but reduced appetite and other factors may impact on their intake. At home, oral feeding is usually delivered by parents; so involving parents more actively during the mealtimes in PICU may contribute to improved patient/family satisfaction. We aimed to assess the impact of a new “room service” initiative involving parents on mealtime quality and on both family and healthcare professional (HCP) satisfaction. Methods: A prospective, single centre, before and after intervention study was designed, as part of a PICU quality of care improvement program in 2013-2016. Two questionnaires assessing oral nutrition practices and family/HCP overall satisfaction were disseminated among the parents of critically ill children capable of oral feeding during their PICU admission and among the whole PICU healthcare professional team (nurses, nurse assistants, and medical doctors). Categorical variables were compared using the chi-square test and Likert scales were compared between groups with the Mann-Whitney-Wilcoxon test. Results: the pre-intervention surveys were completed by 97/130 (75%) HCPs and 52 families, and the post-intervention surveys by 74/130 (57%) HCPs and 54 families. After the intervention, a marked improvement was shown for the overall quality of meal service rating by both HCPs and families (medians and IQR: 5 (5-7) to 7 (7-8) and 6 (6-8) to 8 (7-9) respectively; p<0.01) and also: for the parents’ involvement; in children’s, families’ and healthcare professional satisfaction; in meal dedicated facilities and equipment; and in perception that oral nutrition is an important aspect of PICU care. Conclusions: Implementation of an improved “room service” initiative in the PICU was feasible and improved the perceived quality of care and satisfaction around oral feeding. This family centred care initiative can be integrated in an overall quality improvement strategy

Environmental variables, habitat discontinuity and life history shaping the genetic structure of Pomatoschistus marmoratus

Coastal lagoons are semi-isolated ecosystems exposed to wide fluctuations of environmental conditions and showing habitat fragmentation. These features may play an important role in separating species into different populations, even at small spatial scales. In this study, we evaluate the concordance between mitochondrial (previous published data) and nuclear data analyzing the genetic variability of Pomatoschistus marmoratus in five localities, inside and outside the Mar Menor coastal lagoon (SE Spain) using eight microsatellites. High genetic diversity and similar levels of allele richness were observed across all loci and localities, although significant genic and genotypic differentiation was found between populations inside and outside the lagoon. In contrast to the FST values obtained from previous mitochondrial DNA analyses (control region), the microsatellite data exhibited significant differentiation among samples inside the Mar Menor and between lagoonal and marine samples. This pattern was corroborated using Cavalli-Sforza genetic distances. The habitat fragmentation inside the coastal lagoon and among lagoon and marine localities could be acting as a barrier to gene flow and contributing to the observed genetic structure. Our results from generalized additive models point a significant link between extreme lagoonal environmental conditions (mainly maximum salinity) and P. marmoratus genetic composition. Thereby, these environmental features could be also acting on genetic structure of coastal lagoon populations of P. marmoratus favoring their genetic divergence. The mating strategy of P. marmoratus could be also influencing our results obtained from mitochondrial and nuclear DNA. Therefore, a special consideration must be done in the selection of the DNA markers depending on the reproductive strategy of the species

Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range

publishedVersionPaid Open AccessUNIT agreemen

Should We Abandon the t-Test in the Analysis of Gene Expression Microarray Data: A Comparison of Variance Modeling Strategies

High-throughput post-genomic studies are now routinely and promisingly investigated in biological and biomedical research. The main statistical approach to select genes differentially expressed between two groups is to apply a t-test, which is subject of criticism in the literature. Numerous alternatives have been developed based on different and innovative variance modeling strategies. However, a critical issue is that selecting a different test usually leads to a different gene list. In this context and given the current tendency to apply the t-test, identifying the most efficient approach in practice remains crucial. To provide elements to answer, we conduct a comparison of eight tests representative of variance modeling strategies in gene expression data: Welch's t-test, ANOVA [1], Wilcoxon's test, SAM [2], RVM [3], limma [4], VarMixt [5] and SMVar [6]. Our comparison process relies on four steps (gene list analysis, simulations, spike-in data and re-sampling) to formulate comprehensive and robust conclusions about test performance, in terms of statistical power, false-positive rate, execution time and ease of use. Our results raise concerns about the ability of some methods to control the expected number of false positives at a desirable level. Besides, two tests (limma and VarMixt) show significant improvement compared to the t-test, in particular to deal with small sample sizes. In addition limma presents several practical advantages, so we advocate its application to analyze gene expression data

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement