Occupancy modelling as a new approach to assess supranational trends using opportunistic data: a pilot study for the damselfly Calopteryx splendens

There is limited information available on changes in biodiversity at the European scale, because there is a lack of data from standardised monitoring for most species groups. However, a great number of observations made without a standardised field protocol is available in many countries for many species. Such opportunistic data offer an alternative source of information, but unfortunately such data suffer from non-standardised observation effort and geographical bias. Here we describe a new approach to compiling supranational trends using opportunistic data which adjusts for these two major imperfections. The non-standardised observation effort is dealt with by occupancy modelling, and the unequal geographical distribution of sites by a weighting procedure. The damselfly Calopteryx splendens was chosen as our test species. The data were collected from five countries (Ireland, Great Britain, the Netherlands, Belgium and France), covering the period 1990–2008. We used occupancy models to estimate the annual number of occupied 1 × 1 km sites per country. Occupancy models use presence-absence data, account for imperfect detection of species, and thereby correct for between-year variability in observation effort. The occupancy models were run per country in a Bayesian mode of inference using JAGS. The occupancy estimates per country were then aggregated to assess the supranational trend in the number of occupied 1 × 1 km². To adjust for the unequal geographical distribution of surveyed sites, we weighted the countries according to the number of sites surveyed and the range of the species per country. The distribution of C. splendens has increased significantly in the combined five countries. Our trial demonstrated that a supranational trend in distribution can be derived from opportunistic data, while adjusting for observation effort and geographical bias. This opens new perspectives for international monitoring of biodiversity.     

Nonparametric correction for covariate measurement error in a stratified Cox model

Stratified Cox regression models with large number of strata and small stratum size are useful in many settings, including matched case-control family studies. In the presence of measurement error in covariates and a large number of strata, we show that extensions of existing methods fail either to reduce the bias or to correct the bias under nonsymmetric distributions of the true covariate or the error term. We propose a nonparametric correction method for the estimation of regression coefficients, and show that the estimators are asymptotically consistent for the true parameters. Small sample properties are evaluated in a simulation study. The method is illustrated with an analysis of Framingham data.     

The 102-Kilobase Unstable Region of Yersinia pestis Comprises a High-Pathogenicity Island Linked to a Pigmentation Segment Which Undergoes Internal Rearrangement

Several pathogenicity islands have recently been identified in different bacterial species, including a high-pathogenicity island (HPI) in Yersinia enterocolitica 1B. In Y. pestis, a 102-kb chromosomal fragment (pgm locus) that carries genes involved in iron acquisition and colony pigmentation can be deleted en bloc. In this study, characterization and mapping of the 102-kb region of Y. pestis 6/69 were performed to determine if this unstable region is a pathogenicity island. We found that the 102-kb region of Y. pestis is composed of two clearly distinct regions: an ≈35-kb iron acquisition segment, which is an HPI per se, linked to an ≈68-kb pigmentation segment. This linkage was preserved in all of the Y. pestis strains studied. However, several nonpigmented Y. pestis strains harboring an irp2 gene have been previously identified, suggesting that the pigmentation segment is independently mobile. Comparison of the physical map of the 102-kb region of these strains with that of strain 6/69 and complementation experiments were carried out to determine the genetic basis of this phenomenon. We demonstrate that several different mechanisms involving mutations and various-size deletions are responsible for the nonpigmented phenotype in the nine strains studied. However, no deletion corresponded exactly to the pigmentation segment. The 102-kb region of Y. pestis is an evolutionarily stable linkage of an HPI with a pigmentation segment in a region of the chromosome prone to rearrangement in vitro.     

Analysis of the N-acetylneuraminic acid and N-glycolylneuraminic acid contents of glycoproteins by high-pH anion-exchange chromatography with pulsed amperometric detection

Presence or absence of N-acetylneuraminic acid (Neu5Ac) can change a sialylated glycoprotein's serum half-life and possibly its function. We evaluated the linearity, sensitivity, reproducibility, and accuracy of a HPAEC/PAD method to determine its suitability for routine simultaneous analysis of Neu5Ac and N-glycolylneuraminic acid (Neu5Gc). An effective internal standard for this analysis is 3-deoxy-d-glycero-d- galacto-2-nonulosonic acid (KDN). We investigated the effect of the Au working electrode recession and determined that linear range and sensitivity were dependent on electrode recession. Using an electrode that was 350 &mgr;m recessed from the electrode block, the minimum detection limits of Neu5Ac, KDN, and Neu5Gc were 2, 5, and 2 pmol, respectively, and were reduced to 1, 2, and 0.5 pmol using a new electrode. The response of standards was linear from 10 to 500 pmol (r2>0.99) regardless of electrode recession. When Neu5Ac, KDN, and Neu5Gc (200 pmol each) were analyzed repetitively for 48 h, area RSDs were <3%. Reproducibility was unaffected when injections of glycoprotein neuraminidase and acid digestions were interspersed with standard injections. Area RSDs of Neu5Ac and Neu5Gc improved when the internal standard was used. We determined the precision and accuracy of this method for both a recessed and a new working electrode by analyzing Neu5Ac and Neu5Gc contents of bovine fetuin and bovine and human transferrins. Results were consistent with published values and independent of the working electrode. The sensitivity, reproducibility, and accuracy of this method make it suitable for direct routine analysis of glycoprotein Neu5Ac and Neu5Gc contents.