Identification of the different sources responsible for olfactory annoyance, using an e-nose

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Modelling trace metal background to evaluate anthropogenic contamination in arable soils of south-western France

The trace metal (TM) content in arable soils has been monitored across a region of France characterised by a large proportion of calcareous soils. Within this particular geological context, the objectives were to first determine the natural levels of trace metals in the soils and secondly, to assess which sites were significantly contaminated. Because no universal contamination assessment method is currently available, four different methods were applied and compared in order to facilitate the best diagnosis of contamination. First, the TM geochemical background was determined by using basic descriptive statistics and linear regression models calculated with semi-conservative major elements as predictors. The natural concentrations of trace metals varied greatly due to the high soil heterogeneity encountered on the regional scale and were more-or-less accurately modelled according to the considered TM. Second, the basic descriptive statistics and the linear regression methods were then compared with the enrichment factor (EF) method and multivariate analysis (PCA), in order to evaluate whether the concentrations measured in soils were abnormally high or not. The advantages and disadvantages of each method were discussed and their results used to identify the most probable contamination cases, the influence of the soils characteristics, as well as the agricultural land cover. The basic descriptive method was good as a first and easy approach to describe the TM ambient concentrations, but may misinterpret the natural anomalies as contaminations. Based on geochemical associations, the linear regression method provided more realistic results even if the relationships between major and trace metals were not significant for the most mobile TM. The EF method was useful to identify high point source contaminations, but it was not suitable when considering a large dataset of low TM concentrations. Finally, the PCA method was a good preliminary tool for the description of the global TM concentrations in a studied area, but it could only give indication on the highest contaminated points. By comparing the results of the different methods in the studied region, we estimated that 24% of the arable soils were contaminated by at least one trace metal, mainly Cu in vineyards/orchards and Cd, Pb and/or Zn in grazing lands. In addition, the calcareous soils exhibited globally higher natural and anthropogenic TM concentrations than non-calcareous soils, probably because of the lower TM mobility at alkaline pH

Condition aux limites transparente pour la propagation acoustique dans un guide recouvert d'un matériau absorbant en présence d'un écoulement uniforme

L'objet de notre travail est de calculer par éléments finis le rayonnement acoustique dans un guide d'onde infini dont une paroi est recouverte d'un matériau absorbant, caractérisé par une impédance Z. Pour tronquer le domaine de calcul, on veut introduire des conditions aux limites transparentes déduites d'une décomposition modale, ce qui nécessite la détermination des modes du guide. En l'absence d'écoulement, la décomposition est aisée pour un guide à parois rigides. En présence d'un matériau absorbant, de nombreuses difficultés apparaissent même en l'absence d'écoulement : l'opérateur n'est plus auto-adjoint et les modes ne sont plus orthogonaux pour le produit scalaire usuel. On montre qu'on peut introduire un « produit scalaire particulier » qui conduit à une « pseudo orthogonalité des modes ». Toutefois, on montre qu'il existe une suite de valeurs « exceptionnelles » de l'impédance Zc pour lesquelles la décomposition modale n'est pas possible. La méthode est étendue au cas d'un écoulement uniforme. L'apparition de dérivées tangentielles de la pression sur la paroi traitée entraîne des difficultés supplémentaires. Un nouveau produit scalaire est introduit, incluant les valeurs de la pression sur la paroi traitée. On montre alors que les modes ne deviennent orthogonaux que si l'un des modes est d'indice élevé et que cette propriété suffit pour définir des conditions transparentes. Dans tous les cas, en dehors des valeurs critiques de l'impédance, on se ramène à la résolution d'une équation de dispersion complexe. La méthode de Newton Raphson est utilisée pour l'identification des modes dans le plan complexe. Nous avons développé une méthode numérique pour calculer les modes ou le rayonnement d'une source, basée sur le couplage entre des éléments finis et les conditions transparentes. Les simulations sont en bon accord, soit avec les résultats analytiques pour les modes, soit avec la pression rayonnée obtenue par une méthode alternative : en entourant le domaine de calcul par des couches absorbantes de type PML (Perfectly Matched Layers)

Copy number variations and risk for schizophrenia in 22q11.2 deletion syndrome

22q11.2 Deletion Syndrome (22q11.2DS) is a common microdeletion syndrome with congenital and late-onset features. Testing for the genomic content of copy number variations (CNVs) may help elucidate the 22q11.2 deletion mechanism and the variable clinical expression of the syndrome including the high (25%) risk for schizophrenia. We used genome-wide microarrays to assess CNV content and the parental origin of 22q11.2 deletions in a cohort of 100 adults with 22q11.2DS (44 with schizophrenia) and controls. 22q11.2DS subjects with schizophrenia failed to exhibit de novo CNVs or any excess of novel inherited CNVs outside the 22q11.2 region. There were no significant effects of parental origin of the 22q11.2 deletion, deletion length, parental age or family history on expression of schizophrenia. There was no evidence for a general increase of de novo CNVs in 22q11.2DS. A novel finding was the relative paucity of males with de novo 22q11.2 deletions of paternal origin (P = 0.019). The Y chromosome may play a mediating role in the mechanism of 22q11.2 deletion events during spermatogenesis, resulting in the previously observed excess of maternal de novo 22q11.2 deletions. Hemizygosity of the 22q11.2 region appears to be the major CNV-related risk factor for schizophrenia in 22q11.2DS. The results reinforce the need for further efforts to identify specific molecular mechanisms underlying this expression and to identify the 1% of patients with schizophrenia who carry 22q11.2 deletions

Antistaphylococcal activity of DNA-interactive pyrrolobenzodiazepine (PBD) dimers and PBD-biaryl conjugates

Objectives: pyrrolobenzodiazepine (PBD) dimers, tethered through inert propyldioxy or pentyldioxy linkers, possess potent bactericidal activity against a range of Gram-positive bacteria by virtue of their capacity to cross-link duplex DNA in sequence-selective fashion. Here we attempt to improve the antibacterial activity and cytotoxicity profile of PBD-containing conjugates by extension of dimer linkers and replacement of one PBD unit with phenyl-substituted or benzo-fused heterocycles that facilitate non-covalent interactions with duplex DNA.Methods: DNase I footprinting was used to identify high-affinity DNA binding sites. A staphylococcal gene microarray was used to assess epidemic methicillin-resistant Staphylococcus aureus 16 phenotypes induced by PBD conjugates. Molecular dynamics simulations were employed to investigate the accommodation of compounds within the DNA helix.Results: increasing the length of the linker in PBD dimers led to a progressive reduction in antibacterial activity, but not in their cytotoxic capacity. Complex patterns of DNA binding were noted for extended PBD dimers. Modelling of DNA strand cross-linking by PBD dimers indicated distortion of the helix. A majority (26 of 43) of PBD-biaryl conjugates possessed potent antibacterial activity with little or no helical distortion and a more favourable cytotoxicity profile. Bactericidal activity of PBD-biaryl conjugates was determined by inability to excise covalently bound drug molecules from bacterial duplex DNA.Conclusions: PBD-biaryl conjugates have a superior antibacterial profile compared with PBD dimers such as ELB-21. We have identified six PBD-biaryl conjugates as potential drug development candidate

Rare variation at the TNFAIP3 locus and susceptibility to rheumatoid arthritis

Genome-wide association studies (GWAS) conducted using commercial single nucleotide polymorphisms (SNP) arrays have proven to be a powerful tool for the detection of common disease susceptibility variants. However, their utility for the detection of lower frequency variants is yet to be practically investigated. Here we describe the application of a rare variant collapsing method to a large genome-wide SNP dataset, the Wellcome Trust Case Control Consortium rheumatoid arthritis (RA) GWAS. We partitioned the data into gene-centric bins and collapsed genotypes of low frequency variants (defined here as MAF ≤0.05) into a single count coupled with univariate analysis. We then prioritised gene regions for further investigation in an independent cohort of 3,355 cases and 2,427 controls based on rare variant signal p value and prior evidence to support involvement in RA. A total of 14,536 gene bins were investigated in the primary analysis and signals mapping to the TNFAIP3 and chr17q24 loci were selected for further investigation. We detected replicating association to low frequency variants in the TNFAIP3 gene (combined p = 6.6 × 10−6). Even though rare variants are not well-represented and can be difficult to genotype in GWAS, our study supports the application of low frequency variant collapsing methods to genome-wide SNP datasets as a means of exploiting data that are routinely ignored

Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits

Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design. Here we report initial results from a participant-driven study of 22 traits. Replications of associations (in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, TYR, TYRP1, ASIP, and MC1R) for hair color, eye color, and freckling validate the Web-based, self-reporting paradigm. The identification of novel associations for hair morphology (rs17646946, near TCHH; rs7349332, near WNT10A; and rs1556547, near OFCC1), freckling (rs2153271, in BNC2), the ability to smell the methanethiol produced after eating asparagus (rs4481887, near OR2M7), and photic sneeze reflex (rs10427255, near ZEB2, and rs11856995, near NR2F2) illustrates the power of the approach

High-Throughput High-Resolution Class I HLA Genotyping in East Africa

HLA, the most genetically diverse loci in the human genome, play a crucial role in host-pathogen interaction by mediating innate and adaptive cellular immune responses. A vast number of infectious diseases affect East Africa, including HIV/AIDS, malaria, and tuberculosis, but the HLA genetic diversity in this region remains incompletely described. This is a major obstacle for the design and evaluation of preventive vaccines. Available HLA typing techniques, that provide the 4-digit level resolution needed to interpret immune responses, lack sufficient throughput for large immunoepidemiological studies. Here we present a novel HLA typing assay bridging the gap between high resolution and high throughput. The assay is based on real-time PCR using sequence-specific primers (SSP) and can genotype carriers of the 49 most common East African class I HLA-A, -B, and -C alleles, at the 4-digit level. Using a validation panel of 175 samples from Kampala, Uganda, previously defined by sequence-based typing, the new assay performed with 100% sensitivity and specificity. The assay was also implemented to define the HLA genetic complexity of a previously uncharacterized Tanzanian population, demonstrating its inclusion in the major East African genetic cluster. The availability of genotyping tools with this capacity will be extremely useful in the identification of correlates of immune protection and the evaluation of candidate vaccine efficacy

National trends in total cholesterol obscure heterogeneous changes in HDL and non-HDL cholesterol and total-to-HDL cholesterol ratio : a pooled analysis of 458 population-based studies in Asian and Western countries

Background: Although high-density lipoprotein (HDL) and non-HDL cholesterol have opposite associations with coronary heart disease, multi-country reports of lipid trends only use total cholesterol (TC). Our aim was to compare trends in total, HDL and nonHDL cholesterol and the total-to-HDL cholesterol ratio in Asian and Western countries. Methods: We pooled 458 population-based studies with 82.1 million participants in 23 Asian and Western countries. We estimated changes in mean total, HDL and non-HDL cholesterol and mean total-to-HDL cholesterol ratio by country, sex and age group. Results: Since similar to 1980, mean TC increased in Asian countries. In Japan and South Korea, the TC rise was due to rising HDL cholesterol, which increased by up to 0.17 mmol/L per decade in Japanese women; in China, it was due to rising non-HDL cholesterol. TC declined in Western countries, except in Polish men. The decline was largest in Finland and Norway, at similar to 0.4 mmol/L per decade. The decline in TC in most Western countries was the net effect of an increase in HDL cholesterol and a decline in non-HDL cholesterol, with the HDL cholesterol increase largest in New Zealand and Switzerland. Mean total-to-HDL cholesterol ratio declined in Japan, South Korea and most Western countries, by as much as similar to 0.7 per decade in Swiss men (equivalent to similar to 26% decline in coronary heart disease risk per decade). The ratio increased in China. Conclusions: HDL cholesterol has risen and the total-to-HDL cholesterol ratio has declined in many Western countries, Japan and South Korea, with only a weak correlation with changes in TC or non-HDL cholesterol.Peer reviewe