Field studies on the population dynamics of Biomphalaria glabrata, intermediate host of Schistosoma mansoni on the West Indian Island of St. Lucia

Growth curves, calculated for field populations of B. glabrata, were not materially affected by habitat, altitude or season. A mean growth curve was therefore used to estimate the age-frequency distribution of snails in successive field samples. These data permitted the construction of ecological life tables and the estimation of r, the intrinsic rate of natural increase (or decrease) of the different populations. The calculated values of r were inserted in a simple model of unlimited population growth but the resultant curves poorly represented the observed data. A model for unlimited growth was more satisfactory for pond and marsh populations but, apparently, immigration made it less satisfactory for stream and banana drain populations. Nevertheless, r may still be of value in predicting repopulation rates in certain habitats after a mollusciciding which does not kill the entire snail population.     

Uncertainty associated with river health assessment in a varying environment: The case of a predictive fish-based index in France

Sensitive biological measures of river ecosystem quality are needed to assess, maintain or restore ecological conditions of water bodies. Since our understanding of these complex systems is imperfect, decision-making requires recognizing uncertainty. In this study, a new predictive multi-metric index based on fish functional traits was developed to assess French rivers. Information on fish assemblage structure, local environment and human-induced disturbances of 1654 French river sites was compiled. A Bayesian framework was used to predict theoretical metric values in absence of human pressure and to estimate the uncertainty associated with these predictions. The uncertainty associated with the index score gives the confidence associated with the evaluation of site ecological conditions.Among the 228 potential metrics tested, only 11 were retained for the index computation. The final index is independent from natural variability and sensitive to human-induced disturbances. In particular, it is affected by the accumulation of different degradations and specific degradations including hydrological perturbations. Predictive uncertainty is globally lower for IPR+ than for underlying metrics.This new methodology seems appropriate to develop bio-indication tools accounting for uncertainty related to reference condition definition and could be extended to other biological groups and areas. Our results support the use of multi-metric indexes to assess rivers and strengthen the idea that examination of uncertainty could contribute greatly to the improvement of the assessment power of bio-indicators.     

Stand height and cover type complement forest age structure as a biodiversity indicator in boreal and northern temperate forest management

Forest age structure is one of the main indicators of biodiversity in temperate and boreal forests worldwide. This indicator was mainly chosen for the conservation of a subset of rare or sensitive species related to the oldest age classes, not to capture variability across the entire biodiversity spectrum, but is often considered as such. In this study, we analysed alpha and beta diversity in temporary plots of western Quebec, Canada, to consider biodiversity indicators complementary to existing forest age structure targets. Our analysis revealed that considered individually, stand characteristics such as cover type and height are better predictors of changes in site-level contribution to tree beta diversity than age. We also show that plots belonging to different age classes can be similar in terms of tree alpha diversity. Height class was found to have a more significant impact on tree alpha diversity than expected: height was more important than age in coniferous forests, and in deciduous and mixedwood stands it frequently complemented age in explaining the observed diversity patterns. Our results suggest that forest age structure target levels should not be used as the sole indicator of ecosystem sustainability, and that some mature secondary stands can provide significant contributions to biodiversity. We propose that more efficient trade-offs between forest exploitation, ecosystem functioning and environmental conservation can be attained if: (i) forest age structure targets are complemented by cover type and stand height; or (ii) complementary biodiversity indicators of ecosystem sustainability are implemented.     

Modelling HIV immune response and validation with clinical data

A system of ordinary differential equations is formulated to describe the pathogenesis of HIV infection, wherein certain features that have been shown to be important by recent experimental research are incorporated in the model. These include the role of CD4+memory cells that serve as a major reservoir of latently infected cells, a critical role for T-helper cells in the generation of CD8 memory cells capable of efficient recall response, and stimulation by antigens other than HIV. A stability analysis illustrates the capability of this model in admitting multiple locally asymptotically stable (locally a.s.) off-treatment equilibria. We show that this more biologically detailed model can exhibit the phenomenon of transient viremia experienced by some patients on therapy with viral load levels suppressed below the detection limit. We also show that the loss of CD4+T-cell help in the generation of CD8+memory cells leads to larger peak values for the viral load during transient viremia. Censored clinical data is used to obtain parameter estimates. We demonstrate that using a reduced set of 16 free parameters, obtained by fixing some parameters at their population averages, the model provides reasonable fits to the patient data and, moreover, that it exhibits good predictive capability. We further show that parameter values obtained for most clinical patients do not admit multiple locally a.s off-treatment equilibria. This suggests that treatment to move from a high viral load equilibrium state to an equilibrium state with a lower (or zero) viral load is not possible for these patients.     

Planktonic indices in the evaluation of the ecological status and the trophic state of the longest lake in Poland

Due to the intensive mixing polymictic lakes should be homogenous. However, morphometric diversity and high water dynamics contribute to the differentiation of many parameters in various areas of the lakes. This study analyzes both phytoplankton and zooplankton to assess differences in water quality along the north–south axis of the longest lake in Poland. New phytoplankton indicators were applied for determining the lake's ecological status: the Q index based on functional groups and the PMPL (Phytoplankton Metric for Polish Lakes) index based on phytoplankton biomass. TSI_ROT index (Rotifer Trophic State Index), which comprises the percentage of species indicating a high trophic state in the indicatory group and the percentage of bacteriovorus in the Rotifera population, was used for zooplankton analysis.TP content was different at different sites – we observed its gradual increase from the south to the north. Spatial variation of phosphorus did not considerably affect plankton diversity. The phytoplankton was dominated by Oscillatoriales, typical of shallow, well-mixed eutrophic lakes. The ecological status of the lake based on the EQR (Ecological Quality Ratio) was poor or moderate. The zooplankton was dominated by rotifers (at almost all sites), which indicates a eutrophic state of the lake. The values of phytoplankton indices at the studied sites did not differ considerably; the differences resulted more from local conditions such as the contaminant inflow and the macrophyte development than water dynamics.We have demonstrated that in the lake dominated by filamentous Cyanobacteria the ecological status should be determined according to the PMPL index or other indices dependent on the dominant Cyanobacteria species. Since the Q index does not include the functional group S1, the results can lead to the false conclusion that water quality improves with an increased amount of phytoplankton. The high abundance of Cyanobacteria in the lake may have contributed to the poor growth of rotifers.     

Factors encoded by and affecting the holding stability of yeast plasmid pSR1

Summary A 2 m DNA-like plasmid, pSR1, isolated from a strain of Zygosaccharomyces rouxii has three coding frames, P, S and R. Insertional inactivation of R completely abolished the intramolecular recombination, and the defect was complemented by an intact R frame on a coexistent plasmid molecule. The P and S regions were also transactive and important, but not essential, for the stable maintenance of the plasmid molecules. Insertional disruption of the P frame suggested that it produces a protein factor. Similar insertional disruption of the S frame affected the plasmid stability in Z. rouxii and Saccharomyces cerevisiae hosts differently, depending on whether the inserted DNA fragment was a short 8 bp SalI linker or a long (2.2 kb) DNA fragment. Results strongly suggested that the S region encodes two factors, one RNA and the other a protein, and that the S protein is compatible with a sprecific hostfactor in Z. rouxii, but not in S. cerevisiae. In addition, a cis-acting locus, Z, was found at a site in the plasmid molecule where no distinct open reading frames were located. No long direct repeats or inverted repeats were observed in the Z region, such as are found in the REP3 locus of 2 m DNA.     

Prediction of the tertiary structure of the alpha-subunit of tryptophan synthase

The tertiary structure of the alpha-subunit of tryptophan synthase was proposed using a combination of experimental data and computational methods. The vacuum-ultraviolet circular dichroism spectrum was used to assign the protein to the alpha/beta-class of supersecondary structures. The two-domain structure of the alpha-subunit (Miles et al.: Biochemistry 21:2586, 1982; Beasty and Matthews: Biochemistry 24:3547, 1985) eliminated consideration of a barrel structure and focused attention on a beta-sheet structure. An algorithm (Cohen et al.: Biochemistry 22:4894, 1983) was used to generate a secondary structure prediction that was consistent with the sequence data of the alpha-subunit from five species. Three potential secondary structures were then packed into tertiary structures using other algorithms. The assumption of nearest neighbors from second-site revertant data eliminated 97% of the possible tertiary structures; consideration of conserved hydrophobic packing regions on the beta-sheet eliminated all but one structure. The native structure is predicted to have a parallel beta-sheet flanked on both sides by alpha-helices, and is consistent with the available data on chemical cross-linking, chemical modification, and limited proteolysis. In addition, an active site region containing appropriate residues could be identified as well as an interface for beta 2-subunit association. The ability of experimental data to facilitate the prediction of protein structure is discussed.