A Bayesian analysis of multivariate doubly-interval-censored dental data

A Bayesian survival analysis is presented to examine the effect of fluoride-intake on the time to caries development of the permanent first molars in children between 7 and 12 years of age using a longitudinal study conducted in Flanders. Three problems needed to be addressed. Firstly, since the emergence time of a tooth and the time it experiences caries were recorded yearly, the time to caries is doubly interval censored. Secondly, due to the setup of the study, many emergence times were left-censored. Thirdly, events on teeth of the same child are dependent. Our Bayesian analysis is a modified version of the intensity model of Harkanen et al. (2000, Scandinavian Journal of Statistics 27, 577-588). To tackle the problem of the large number of left-censored observations a similar Finnish data set was introduced. Our analysis shows no convincing effect of fluoride-intake on caries development.     

Biogeochemistry of selenium and its impact on food chain quality and human health

In areas where soils are low in bioavailable selenium (Se), potential Se deficiencies cause health risks for humans. Though higher plants have been considered not to require this element, the experience with low-Se soils in Finland has provided evidence that the supplementation of commercial fertilizers with sodium selenate affects positively not only the nutritive value of the whole food chain from soil to plants, animals and humans but also the quantity of plant yields. The level of Se addition has been optimal, and no abnormally high concentrations in plants or in foods of animal origin have been observed. Se levels in serum and human milk indicate that the average daily intake has been within limits considered to be safe and adequate. In fact, plants act as effective buffers, because their growth is reduced at high Se levels. They also tend to synthesize volatile compounds in order to reduce excess Se. On the other hand, when added at low concentrations, Se exerts a beneficial effect on plant growth via several mechanisms. As in humans and animals, Se strengthens the capacity of plants to counteract oxidative stress caused by oxygen radicals produced by internal metabolic or external factors. At proper levels it also delays some of the effects of senescence and may improve the utilization of short-wavelength light by plants. High additions are toxic and may trigger pro-oxidative reactions. Thus, the present supplementation of fertilizers with Se can be considered a very effective and readily controlled way to increase the average daily Se intake nationwide.     

Agronomic biofortification of Brassica with selenium—enrichment of SeMet and its identification in Brassica seeds and meal

Selenium (Se) is an essential micronutrient and is circulated to the food chain through crops. Brassica species are efficient in Se accumulation and thus, good species for Se biofortification purposes. The residual fraction obtained after oil processing of Brassica seeds, the meal, is an important protein source in animal diets and used in feed concentrates. The accumulation of soil or foliar applied Se in the seeds and meal of Brassica napus and B. rapa as well as its effects on growth and yield formation was studied in two field experiments. Also, a HPLC-ICP-MS based method for the identification and quantification of Se species in Brassica seeds and meal was developed. Selenium application did not affect the yield or oil content. High accumulation of Se in the seeds and meal (1.92–1.96 μg Se g^?1) was detected. Biotransformation of inorganic Se was evaluated by using HPLC-ICP-MS previous enzymatic hydrolysis for species extraction. The Se speciation studies showed that up to 85% of the total Se was SeMet whereas other Se-species were not detected. We conclude that the agronomic biofortification of Brassica species can improve the nutritive quality of the protein rich meal fraction as it contains significant amount of SeMet.     

Small Tails Tell Tall Tales – Intra-Individual Variation in the Stable Isotope Values of Fish Fin

Background

Fish fin is a widely used, non-lethal sample material in studies using stable isotopes to assess the ecology of fishes. However, fish fin is composed of two distinct tissues (ray and membrane) which may have different stable isotope values and are not homogeneously distributed within a fin. As such, estimates of the stable isotope values of a fish may vary according to the section of fin sampled.

Methods

To assess the magnitude of this variation, we analysed carbon (δ ¹³C), nitrogen (δ ¹⁵N), hydrogen (δ ²H) and oxygen (δ ¹⁸O) stable isotopes of caudal fin from juvenile, riverine stages of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). Individual fins were sub-sectioned into tip, mid and base, of which a further subset were divided into ray and membrane.

Findings

Isotope variation between fin sections, evident in all four elements, was primarily related to differences between ray and membrane. Base sections were¹³C depleted relative to tip (~ 1 ‰) with equivalent variation evident between ray and membrane. A similar trend was evident in δ ²H, though the degree of variation was far greater (~ 10 ‰). Base and ray sections were ¹⁸O enriched (~ 2 ‰) relative to tip and membrane, respectively. Ray and membrane sections displayed longitudinal variation in ¹⁵N mirroring that of composite fin (~ 1 ‰), indicating that variation in¹⁵N values was likely related to ontogenetic variation.

Conclusions

To account for the effects of intra-fin variability in stable isotope analyses we suggest that researchers sampling fish fin, in increasing priority, 1) also analyse muscle (or liver) tissue from a subsample of fish to calibrate their data, or 2) standardize sampling by selecting tissue only from the extreme tip of a fin, or 3) homogenize fins prior to analysis.     

Determinants of parasitoid communities of willow‐galling sawflies: habitat overrides physiology,host plant and space

Studies on the determinants of plant–herbivore and herbivore–parasitoid associations provide important insights into the origin and maintenance of global and local species richness. If parasitoids are specialists on herbivore niches rather than on herbivore taxa, then alternating escape of herbivores into novel niches and delayed resource tracking by parasitoids could fuel diversification at both trophic levels. We used DNA barcoding to identify parasitoids that attack larvae of seven Pontania sawfly species that induce leaf galls on eight willow species growing in subarctic and arctic–alpine habitats in three geographic locations in northern Fennoscandia, and then applied distance‐ and model‐based multivariate analyses and phylogenetic regression methods to evaluate the hierarchical importance of location, phylogeny and different galler niche dimensions on parasitoid host use. We found statistically significant variation in parasitoid communities across geographic locations and willow host species, but the differences were mainly quantitative due to extensive sharing of enemies among gallers within habitat types. By contrast, the divide between habitats defined two qualitatively different network compartments, because many common parasitoids exhibited strong habitat preference. Galler and parasitoid phylogenies did not explain associations, because distantly related arctic–alpine gallers were attacked by a species‐poor enemy community dominated by two parasitoid species that most likely have independently tracked the gallers’ evolutionary shifts into the novel habitat. Our results indicate that barcode‐ and phylogeny‐based analyses of food webs that span forested vs. tundra or grassland environments could improve our understanding of vertical diversification effects in complex plant–herbivore–parasitoid networks.     

Crystal structures of Trichoderma reesei β-galactosidase reveal conformational changes in the active site

We have determined the crystal structure of Trichoderma reesei (Hypocrea jecorina) β-galactosidase (Tr-β-gal) at a 1.2? resolution and its complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4? resolutions, respectively. Tr-β-gal is a potential enzyme for lactose hydrolysis in the dairy industry and belongs to family 35 of the glycoside hydrolases (GH-35). The high resolution crystal structures of this six-domain enzyme revealed interesting features about the structure of Tr-β-gal. We discovered conformational changes in the two loop regions in the active site, implicating a conformational selection-mechanism for the enzyme. In addition, the Glu200, an acid/base catalyst showed two different conformations which undoubtedly affect the pK(a) value of this residue and the catalytic mechanism. The electron density showed extensive glycosylation, suggesting a structure stabilizing role for glycans. The longest glycan showed an electron density that extends to the eighth monosaccharide unit in the extended chain. The Tr-β-gal structure also showed a well-ordered structure for a unique octaserine motif on the surface loop of the fifth domain.     

Eco-evolutionary dynamics of dispersal in spatially heterogeneous environments

Ecology Letters (2011) 14: 1025-1034 ABSTRACT: Evolutionary changes in natural populations are often so fast that the evolutionary dynamics may influence ecological population dynamics and vice versa. Here we construct an eco-evolutionary model for dispersal by combining a stochastic patch occupancy metapopulation model with a model for changes in the frequency of fast-dispersing individuals in local populations. We test the model using data on allelic variation in the gene phosphoglucose isomerase (Pgi), which is strongly associated with dispersal rate in the Glanville fritillary butterfly. Population-specific measures of immigration and extinction rates and the frequency of fast-dispersing individuals among the immigrants explained 40% of spatial variation in Pgi allele frequency among 97 local populations. The model clarifies the roles of founder events and gene flow in dispersal evolution and resolves a controversy in the literature about the consequences of habitat loss and fragmentation on the evolution of dispersal.     

Genetic variants of TSLP and asthma in an admixed urban population

Background

Thymic stromal lymphopoietin (TSLP), an IL7-like cytokine produced by bronchial epithelial cells is upregulated in asthma and induces dendritic cell maturation supporting a Th2 response. Environmental pollutants, including tobacco smoke and diesel exhaust particles upregulate TSLP suggesting that TSLP may be an interface between environmental pollution and immune responses in asthma. Since asthma is prevalent in urban communities, variants in the TSLP gene may be important in asthma susceptibility in these populations.

Objectives

To determine whether genetic variants in TSLP are associated with asthma in an urban admixed population.

Methodology and Main Results

Ten tag-SNPs in the TSLP gene were analyzed for association with asthma using 387 clinically diagnosed asthmatic cases and 212 healthy controls from an urban admixed population. One SNP (rs1898671) showed nominally significant association with asthma (odds ratio (OR) = 1.50; 95% confidence interval (95% CI): 1.09–2.05, p = 0.01) after adjusting for age, BMI, income, education and population stratification. Association results were consistent using two different approaches to adjust for population stratification. When stratified by smoking status, the same SNP showed a significantly increased risk associated with asthma in ex-smokers (OR = 2.00, 95% CI: 1.04–3.83, p = 0.04) but not significant in never-smokers (OR = 1.34; 95% CI: 0.93–1.94, p = 0.11). Haplotype-specific score test indicated that an elevated risk for asthma was associated with a specific haplotype of TSLP involving SNP rs1898671 (OR = 1.58, 95% CI: 1.10–2.27, p = 0.01). Association of this SNP with asthma was confirmed in an independent large population-based cohort consortium study (OR = 1.15, 95% CI: 1.07–1.23, p = 0.0003) and the results stratified by smoking status were also validated (ex-smokers: OR = 1.21, 95% CI: 1.08–1.34, p = 0.003; never-smokers: OR = 1.06, 95% CI: 0.94–1.17, p = 0.33).

Conclusions

Genetic variants in TSLP may contribute to asthma susceptibility in admixed urban populations with a gene and environment interaction.