In vitro assay to select rainbow trout with variable resistance/susceptibility to viral haemorrhagic septicaemia virus

The merit of a candidate criterion of resistance to viral haemorrhagic septicaemia virus (VHSV) was tested with the view of producing experimental trout progeny with a predictable level of resistance. The criterion, the measure of in vitro viral replication in excised fin tissue (VREFT) was previously developed. Three experiments were performed, using both ordinary and homozygous doubled-haploid breeders. A set of 48 progeny was tested. Breeders were individually scored for repeated measures of VREFT, and the progeny were tested against VHSV (strain 07-71, serotype 1) through a waterborne challenge (5 x 10(4) pfu ml(-1) during 2 h). Analysis of repeated measures of VREFT revealed the risk of identifying 'false' resistant individuals. The highest value should be considered the most predictive of the resistance status. Survival of progeny ranged from 0 to 100% according to the group and the experiment. The survival was correlated to the mean VREFT value of the breeders in Expts 1 and 2 (R = 0.96 and 0.61 respectively), but not in Expt 3 (R = 0.36, ns) where all tested progeny were highly susceptible. Results thus indicate that viral growth in fin tissue is genetically correlated to resistance to waterborne disease and may be used to produce selected progeny, at least at the experimental scale. Possible implications of the relationship between VREFT and resistance for the study of resistance mechanisms are discussed.     

Influence of day-night and tidal cycles on phenol content and antioxidant capacity in three temperate intertidal brown seaweeds

The daily variations of phenol contents and antioxidant capacities were surveyed in a 32-h field experiment in three temperate brown seaweeds belonging to Fucales - Pelvetia canaliculata, Ascophyllum nodosum and Bifurcaria bifurcata - living at different intertidal levels — high-, mid- and low-tide level, respectively. Phenolic compounds of brown seaweeds are secondary metabolites involved in many different protection mechanisms, as for example against grazer and pathogen attack as well as UV damage. This study was thus aimed at understanding the influence of both day/night and tidal cycles on the brown seaweed phenol pool with respect to their bathymetric level on the shore. These cycles affect the quantity and quality of light received by intertidal seaweeds (protection via the water layer during immersion), and the photoprotective role of phlorotannins was thus evaluated. Phenol levels and antioxidant capacities were monitored every hour during a tidal cycle and a half at the equinox spring tide, in March 2003. The three species contained rather high phenol levels, i.e. about 3, 6 and 4% DW in P. canaliculata, A. nodosum and B. bifurcata, respectively. Antioxidant capacities globally paralleled phenol contents in the three species under study. Moreover, the measured antioxidant capacities and the phenol contents of the extracts were significantly and positively correlated in the three species. Significant effect of neither cycles nor their interaction was observed in any species despite a trend to follow day/night alternation for P. canaliculata, and emersion/immersion cycle for A. nodosum. No trend was observed for the third species. However, significant correlations between phenol levels of P. canaliculata and A. nodosum and measured air-temperature were found. Our results suggested an effect of aerial, aquatic and both conditions on the phenolic pool of P. canaliculata, B. bifurcata and A. nodosum, respectively, and a fast evolution of the phenolic pool on a day time scale.     

Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices

Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.     

Structural basis for LEAFY floral switch function and similarity with helix-turn-helix proteins

The LEAFY (LFY) protein is a key regulator of flower development in angiosperms. Its gradually increased expression governs the sharp floral transition, and LFY subsequently controls the patterning of flower meristems by inducing the expression of floral homeotic genes. Despite a wealth of genetic data, how LFY functions at the molecular level is poorly understood. Here, we report crystal structures for the DNA-binding domain of Arabidopsis thaliana LFY bound to two target promoter elements. LFY adopts a novel seven-helix fold that binds DNA as a cooperative dimer, forming base-specific contacts in both the major and minor grooves. Cooperativity is mediated by two basic residues and plausibly accounts for LFY's effectiveness in triggering sharp developmental transitions. Our structure reveals an unexpected similarity between LFY and helix-turn-helix proteins, including homeodomain proteins known to regulate morphogenesis in higher eukaryotes. The appearance of flowering plants has been linked to the molecular evolution of LFY. Our study provides a unique framework to elucidate the molecular mechanisms underlying floral development and the evolutionary history of flowering plants.     

Biomonitoring of urine mutagenicity with the Ames test: improvement of the extraction/concentration method

Comparative extraction efficiency of the pre-packed Bakerbond^®-spe-SDB-1 resin and of Amberlite^®-AD2 (XAD-2) resin, for the preparation of urine extracts in biomonitoring studies. Urine extracts were prepared in parallel with the Bakerbond^® column and with the classical XAD-2 resin from urines (1) spiked with mutagenic chemicals, (2) collected from patients after chemotherapy, and (3) from smokers. Mutagenic activities were evaluated on Salmonella typhimurium tester strains TA97a, TA98, TA100 and TA102 with and without S9 mix. Mutagenic activities obtained with Bakerbond^® extracts were almost always higher or at least equivalent to those prepared on XAD-2 resin. Similar results were observed for the three urine sample groups. When fully validated, the use of the pre-packed columns will be more convenient and time-saving for large population studies.     

Anthropometric and Micronutrient Status of School-Children in an Urban West Africa Setting: A Cross-Sectional Study in Dakar (Senegal)

Background

Urban areas in West Africa are not immune to undernutrition with recent urbanization and high food prices being important factors. School children often have a poor nutritional status, potentially affecting their health and schooling performance. Yet, generally school children do not benefit from nutrition programs. The objective of the study was to assess the anthropometric and micronutrient status of children from state schools in the Dakar area.

Methods

School children (n = 604) aged from 5 to 17 y (52.5% girls, 47.5% ≥10 y) were selected through a two-stage random cluster sample of children attending urban primary state schools in the Dakar area (30 schools × 20 children). The prevalence of stunting (height-for-age<−2 z-scores) and thinness (BMI-for-age<−2 z-scores, WHO 2006, and three grades of thinness corresponding to BMI of 18.5, 17.0 and 16.0 kg/m2 in adults) were calculated from weight and height. Hemoglobin, plasma concentrations of ferritin (FER), transferrin receptors (TfR), retinol binding protein (RBP), and zinc, and urinary iodine concentrations were measured. Correction factors were used for FER and RBP in subjects with inflammation determined with C-reactive protein and α1-acid-glycoprotein.

Results

4.9% of children were stunted, 18.4% were thin, 5.6% had severe thinness (BMI-for-age<−3 z-scores). Only one child had a BMI-for-age>2 z-scores. Prevalence of anemia, iron deficiency and iron deficiency anemia was 14.4%, 39.1% and 10.6% respectively. 3.0% had vitamin A deficiency, 35.9% a marginal vitamin A status, and 25.9% zinc deficiency. Urinary iodine was <50 µg/L in 7.3% of children and ≥200 µg/L in 22.3%. The prevalence of marginal vitamin A, zinc deficiency, high TfR was significantly higher in boys than in girls (P<0.05). Height-for-age and retinol were significantly lower in participants ≥10 y and <10 y respectively.

Conclusion

Undernutrition, especially thinness, iron and zinc deficiencies in school children in the Dakar area requires special targeted nutrition interventions.     

Identifying spatial relationships at multiple scales: principal coordinates of neighbour matrices (PCNM) and geostatistical approaches

We compared two methodological approaches – principal coordinate analysis of neighbour matrices (PCNM) and geostatistics – that both aim at extracting several spatial scales in order to identify spatial relationships between organisms and environmental variables at multiple scales. From a statistical point of view, PCNM analysis and geostatistics come from "two different worlds"– PCNM is based on classical "data analysis" while geostatistical modelling is developed in a probabilistic context. These two methods were used to investigate the spatial relationships between defoliation caused by spruce budworm Choristoneura fumiferana and bioclimatic conditions in Ontario since 1941 through a wide range of scales. On the one hand, PCNM variables related to defoliation frequency were partitioned into four spatial submodels representing respectively four spatial scales: very broad scale (ca>300 km), broad scale (ca 180 km), fine (ca 100 km), and very fine (<80 km). On the other hand, nested variogram modelling was used to identify the relevant scales. The nested variogram model was composed of four variograms with different characteristic scales close to those of the PCNM spatial submodels. Maps of PCNM submodels and kriging components revealed similar spatial patterns of defoliation frequency at very broad and broad scales while spatial patterns at fine and very fine scales looked quite different. Both methods showed that defoliation by spruce budworm occurs at the broader spatial scales but may be explained by fluctuations at the smaller scales. Finally, results based on geostatistics using a Linear Model of Coregionalisation suggested that climatic conditions can be considered to act at the level of outbreak dynamics while the tree community of spruce budworm's principal hosts controls local population dynamics.