Influence of the thermophoresis on aerosol deposition on warm urban surfaces

International audienceIn the case of an accidental or chronic atmospheric pollution by a nuclear plant, aerosols' deposition transfer coefficients must be known. A major issue is to determine the impact of aerosols contained in the radioactive plume on urban areas with the smallest uncertainties

Assessment of Three Mitochondrial Genes (16S, Cytb, CO1) for Identifying Species in the Praomyini Tribe (Rodentia: Muridae)

The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments

PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination

<p>Abstract</p> <p>Background</p> <p>We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by 'Pairwise Identity and Cost Scores Ordination' (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method computes pairwise distances as sequence identities or cost scores, ordinates the resulting distance matrix by means of PCoA, and encodes the principal coordinates as ordered integers. Three biological and 100 simulated datasets were used to assess the performance of the new method.</p> <p>Results</p> <p>Including ambiguous regions coded by means of PICS-Ord increased topological accuracy, resolution, and bootstrap support in real biological and simulated datasets compared to the alternative of excluding such regions from the analysis a priori. In terms of accuracy, PICS-Ord performs equal to or better than previously available methods of ambiguous region coding (e.g., INAASE), with the advantage of a practically unlimited alignment size and increased analytical speed and the possibility of PICS-Ord scores to be analyzed together with DNA data in a partitioned maximum likelihood model.</p> <p>Conclusions</p> <p>Advantages of PICS-Ord over step matrix-based ambiguous region coding with INAASE include a practically unlimited number of OTUs and seamless integration of PICS-Ord codes into phylogenetic datasets, as well as the increased speed of phylogenetic analysis. Contrary to word- and frequency-based methods, PICS-Ord maintains the advantage of pairwise sequence alignment to derive distances, and the method is flexible with respect to the calculation of distance scores. In addition to distance and maximum parsimony, PICS-Ord codes can be analyzed in a Bayesian or maximum likelihood framework. RAxML (version 7.2.6 or higher that was developed for this study) allows up to 32-state ordered or unordered characters. A GTR, MK, or ORDERED model can be applied to analyse the PICS-Ord codes partition, with GTR performing slightly better than MK and ORDERED.</p> <p>Availability</p> <p>An implementation of the PICS-Ord algorithm is available from <url>http://scit.us/projects/ngila/wiki/PICS-Ord</url>. It requires both the statistical software, R <url>http://www.r-project.org</url> and the alignment software Ngila <url>http://scit.us/projects/ngila</url>.</p

Variations of Plasmid Content in Rickettsia felis

Background: Since its first detection, characterization of R. felis has been a matter of debate, mostly due to the contamination of an initial R. felis culture by R. typhi. However, the first stable culture of R. felis allowed its precise phenotypic and genotypic characterization, and demonstrated that this species belonged to the spotted fever group rickettsiae. Later, its genome sequence revealed the presence of two forms of the same plasmid, physically confirmed by biological data. In a recent article, Gillespie et al. ( PLoS One. 2007; 2( 3): e266.) used a bioinformatic approach to refute the presence of the second plasmid form, and proposed the creation of a specific phylogenetic group for R. felis. Methodology/ Principal Findings: In the present report, we, and five independent international laboratories confirmed unambiguously by PCR the presence of two plasmid forms in R. felis strain URRWXCal(2)(T), but observed that the plasmid content of this species, from none to 2 plasmid forms, may depend on the culture passage history of the studied strain. We also demonstrated that R. felis does not cultivate in Vero cells at 37 degrees C but generates plaques at 30 degrees C. Finally, using a phylogenetic study based on 667 concatenated core genes, we demonstrated the position of R. felis within the spotted fever group. Significance: We demonstrated that R. felis, which unambiguously belongs to the spotted fever group rickettsiae, may contain up to two plasmid forms but this plasmid content is unstable

Recent Developments in Fluorescence Correlation Spectroscopy for Diffusion Measurements in Planar Lipid Membranes

Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support

Convergent genetic and expression data implicate immunity in Alzheimer's disease

Background Late–onset Alzheimer's disease (AD) is heritable with 20 genes showing genome wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease we extended these genetic data in a pathway analysis. Methods The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (p = 3.27×10-12 after multiple testing correction for pathways), regulation of endocytosis (p = 1.31×10-11), cholesterol transport (p = 2.96 × 10-9) and proteasome-ubiquitin activity (p = 1.34×10-6). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected p 0.002 – 0.05). Conclusions The immune response, regulation of endocytosis, cholesterol transport and protein ubiquitination represent prime targets for AD therapeutics

Dry deposition velocity of chlorine 36 on grassland

International audienceChlorine 36 (36Cl, T1/2 = 301,000 years) is a radionuclide with natural and anthropogenic origin that can be rejected accidentally during decommissioning of nuclear power plants or chronically during recycling of nuclear waste. Once emitted into the atmosphere, 36Cl (gas and particles) can be transferred to the soil and vegetal cover by dry and wet deposition. However, knowledge of these deposits is very scarce. Because of its relatively high mobility in the geosphere and its high bioavailability, 36Cl fate in the environment should be studied for environmental and human impact assessments.The objective of this work is to determine the dry deposition rates of chlorine 36 on grassland. Grass is studied, as it is a link in the human food chain via cow's milk.In order to achieve this objective, a method for extracting the chlorine contained in plant leaves has been developed. This method consists in heating the dried and grounded plant sample in presence of sodium hydroxide. A temperature gradient up to 450°C allows the extraction to be carried out in two stages: (i) The chlorides with a strong affinity for alkaline environments are first extracted from the plant and preserved in sodium hydroxide; (ii) The organic matter is then destroyed by combustion and the sodium hydroxide crystallised. Brought out from the oven, the dry residue is dissolved in ultrapure water and chemically prepared for the measurement of chlorine 36. This extraction method was validated by its application to NIST standards of peach and apple leaves. The average extraction efficiency of chlorides was 83 ± 3%. For the determination of dry deposition rates, 1m2 of grass was exposed every 2 weeks at the IRSN La Hague technical platform (PTILH) located 2 km downwind from Orano la Hague, a chronic source of low-level chlorine 36 emissions. A mobile shelter with automatic humidity detection covered the grass during rainy episodes. In proximity to the grass, atmospheric chlorine was also sampled at the same frequency as the grass. Gaseous chlorine was sampled by bubbling in sodium hydroxide and by an AS3000 sampler containing activated carbon cartridge. Particulate chlorine was collected on a composite (teflon and glass fibre) filter. Chlorine 36 was measured by accelerated mass spectrometry ASTER (Accelerator for Earth Sciences, Environment and Risks) at CEREGE, Aix-en-Provence, France. All samples were subjected to a succession of chemical preparations in order to remove the sulphur 36 (an isobaric interferent) and to collect the chlorides in the form of AgCl pastilles. The results show a chlorine 36 deposition flux on the grass of 2.94.102 at/m2.s with a deposition velocity in dry weather vd(gas+particles) = 8.10-4 m/s for a contribution of 65.5% of particulate chlorine 36 and 34.5% of gaseous chlorine 36. Based on these experimental results, a modelling of the dry and wet deposits will be carried out considering the parameters related to the canopy and the atmospheric turbulence