Power matters in closing the phenotyping gap

Much of our understanding of physiology and metabolism is derived from investigating mouse mutants and transgenic mice, and open-access platforms for standardized mouse phenotyping such as the German Mouse Clinic (GMC) are currently viewed as one powerful tool for identifying novel gene-function relationships. Phenotyping or phenotypic screening involves the comparison of wild-type control mice with their mutant or transgenic littermates. In our study, we explored the extent to which standardized phenotyping will succeed in detecting biologically relevant phenotypic differences in mice generated and provided by different collaborators. We analyzed quantitative metabolic data (body mass, energy intake, and energy metabolized) collected at the GMC under the current workflow, and used them for statistical power considerations. Our results demonstrate that there is substantial variability in these parameters among lines of wild-type C57BL/6 (B6) mice from different sources. Given this variable background noise in mice that serve as controls, subtle phenotypes in mutant or transgenic littermates may be overlooked. Furthermore, a phenotype observed in one cohort of a mutant line may not be reproducible (to the same extent) in mice coming from a different environment or supplier. In the light of these constraints, we encourage researchers to incorporate information on intrastrain variability into future study planning, or to perform advanced hierarchical analyses. Both will ultimately improve the detectability of novel phenotypes by phenotypic screening. Carola W. Meyer and Ralf Elvert contributed equally to this work.     

Adaptive-filtering of trisomy 21: risk of Down syndrome depends on family size and age of previous child

The neonatal incidence rate of Down syndrome (DS) is well-known to accelerate strongly with maternal age. This non-linearity renders mere accumulation of defects at recombination during prolonged first meiotic prophase implausible as an explanation for DS rate increase with maternal age, but might be anticipated from chromosomal drive (CD) for trisomy 21. Alternatively, as there is selection against genetically disadvantaged embryos, the screening system that eliminates embryos with trisomy 21 might decay with maternal age. In this paper, we provide the first evidence for relaxed filtering stringency (RFS) to represent an adaptive maternal response that could explain accelerating DS rates with maternal age. Using historical data, we show that the proportion of aberrant live births decrease with increased family size in older mothers, that inter-birth intervals are longer before affected neonates than before normal ones, and that primiparae exhibit elevated levels of DS incidence at higher age. These findings are predicted by adaptive RFS but cannot be explained by the currently available alternative non-adaptive hypotheses, including CD. The identification of the relaxation control mechanism and therapeutic restoration of a stringent screen may have considerable medical implications.     

The impact of agroforestry combined with water harvesting on soil carbon and nitrogen stocks in central Chile evaluated using the ICBM/N model

Soil organic carbon (SOC) and total nitrogen (N) stocks in an agroforestry system with water harvesting were analysed in a field experiment and the results compared with those of other crop management systems in the Mediterranean zone of central Chile. Agroforestry with water harvesting showed higher positive effects on N stocks, mainly in the upper soil layer, than the other crop management systems. However, soil analysis revealed a lack of differences between treatments, a fact that might be related mainly to the short study time (12 years) and the high spatial variability in these soil properties at the experimental site. In addition, the Introductory Carbon Balance Model that simulates N processes (ICBM/N) was evaluated for simulating trends in SOC and N stocks in the field experiment. Soil data collected between 1996 and 2008 in the field experiment and primarily literature data sets were used to test ICBM/N and its performance was evaluated by considering uncertainty in model inputs using Generalised Likelihood Uncertainty Estimation (GLUE) methodology. The GLUE estimates (5% and 95%) and measured SOC and N stocks were in satisfactory agreement. The observed SOC and N stocks were bracketed by the uncertainty bands in 70% and 80% of the simulations, respectively. Sensitivity analysis showed the model to be most sensitive to C parameters, such as the humification coefficient (h). The results of this study show that ICBM/N can be an effective tool for estimating SOC and N stocks from agroforestry combined with water harvesting systems in the Mediterranean zone of central Chile over the medium term. However, they also indicate that additional data sets are needed to redefine the parameter distributions in the model and thus to predict trends in SOC and N stocks in the future.     

Monitoring aromatic hydrocarbon biodegradation by functional marker genes

The development of biological treatment technologies for contaminated environments requires tools for obtaining direct information about the biodegradation of specific contaminants. The potential of functional gene array analysis to monitor changes in the amount of functional marker genes as indicators of contaminant biodegradation was investigated. A prototype functional gene array was developed for targeting key functions in the biodegradation of naphthalene, toluene and xylenes. Internal standard probe based normalization was introduced to facilitate comparison across multiple samples. Coupled with one-colour hybridization, the signal normalization improved the consistency among replicate hybridizations resulting in better discrimination for the differences in the amount of target DNA. During the naphthalene biodegradation in a PAH-contaminated soil slurry microcosm, the normalized hybridization signals in naphthalene catabolic gene probes were in good agreement with the amount of naphthalene-degradation genes and the production of 14CO2. Gene arrays provide efficient means for monitoring of contaminant biodegradation in the environment.     

Differences in the growth response of three bryophyte species to nitrogen

The effect of nitrogen on biomass production, shoot elongation and relative density of the mosses Pleurozium schreberi, Hylocomium splendens and Dicranum polysetum was studied in a chamber experiment. Monocultures were exposed to 10 N levels ranging from 0.02 to 7.35 g N m⁻² during a 90-day period. All the growth responses were unimodal, but the species showed differences in the shape parameters of the curves. Hylocomium and Pleurozium achieved optimum biomass production at a lower N level than Dicranum. Pleurozium had the highest biomass production per tissue N concentration. Tolerance to N was the widest in Dicranum, whereas Hylocomium had the narrowest tolerance. Dicranum retained N less efficiently from precipitation than the other two species, which explained its deviating response. All species translocated some N from parent to new shoots. The results emphasize that the individual responses of bryophytes to N should be known when species are used as bioindicators.     

Long-term survey of heavy-metal pollution, biofilm contamination and diatom community structure in the Riou Mort watershed, South-West France

In a metal-polluted stream in the Riou Mort watershed in SW France, periphytic biofilm was analyzed for diatom cell densities and taxonomic composition, dry weight and metal bio-accumulation (cadmium and zinc). Periphytic diatom communities were affected by the metal but displayed induced tolerance, seen through structural impact (dominance of small, adnate species) as well as morphological abnormalities particularly in the genera Ulnaria and Fragilaria. Species assemblages were characterized by taxa known to occur in metal-polluted environments, and shifts in the community structure expressed seasonal patterns: high numbers of Eolimna minima, Nitzschia palea and Pinnularia parvulissima were recorded in Summer and Autumn, whereas the species Surirella brebissonii, Achnanthidium minutissimum, Navicula lanceolata and Surirella angusta were dominant in Winter and Spring. Commonly used indices such as the Shannon diversity index and Specific Pollution Sensitivity Index reflected the level of pollution and suggest seasonal periodicity, the lowest diversities being observed in Summer.     

Sulphur transformation and deposition in the rhizosphere of Juncus effusus in a laboratory-scale constructed wetland

Sulphur cycling and its correlation to removal processes under dynamic redox conditions in the rhizosphere of helophytes in treatment wetlands are poorly understood. Therefore, long-term experiments were performed in laboratory-scale constructed wetlands treating artificial domestic wastewater in order to investigate the dynamics of sulphur compounds, the responses of plants and nitrifying microorganisms under carbon surplus conditions, and the generation of methane. For carbon surplus conditions (carbon:sulphate of 2.8:1) sulphate reduction happened but was repressed, in contrast to unplanted filters mentioned in literature. Doubling the carbon load caused stable and efficient sulphate reduction, rising of pH, increasing enrichment of S(2-) and S(0) in pore water, and finally plant death and inhibition of nitrification by sulphide toxicity. The data show a clear correlation of the occurrence of reduced S-species with decreasing C and N removal performance and plant viability in the experimental constructed wetlands.     

Techniques for the stabilization and assessment of treated copper-, chromium-, and arsenic-contaminated soil

Remediation mainly based on excavation and burial of the contaminated soil is impractical with regard to the large numbers of sites identified as being in need of remediation. Therefore, alternative methods are needed for brownfield remediation. This study was conducted to assess a chemical stabilization procedure of CCA-contaminated soil using iron (Fe)-containing blaster sand (BS) or oxygen-scarfing granulate (OSG). The stabilization technique was assessed with regard to the feasibility of mixing ameliorants at an industrial scale and the efficiency of the stabilization under different redox conditions. The stability was investigated under natural conditions in 1-m3 lysimeters in a field experiment, and the effect of redox conditions was assessed in a laboratory experiment (10 L). The treatments with high additions of ameliorant (8% and 17%) were more successful in both the laboratory and field experiments, even though there was enough Fe on a stochiometric basis even at the lowest addition rates (0.1% and 1%). The particle size of the Fe and the mixing influenced the stabilization efficiency. The development of anaerobic conditions, simulated by water saturation, increases the fraction of arsenic (AsIII) and, consequently, As mobility. The use of high concentrations of OSG under aerobic conditions increased the concentrations of nickel (Ni) and copper (Cu) in the pore water. However, under anaerobic conditions, it decreased the As leaching compared with the untreated soil, and Ni and Cu leaching was not critical. The final destination of the treated soil should govern the amendment choice, that is, an OSG concentration of approximately 10% may be suitable if the soil is to be landfilled under anaerobic conditions. Alternatively, the soil mixed with 1% BS could be kept under aerobic conditions in a landfill cover or in situ at a brownfield site. In addition, the treatment with BS appeared to produce better effects in the long term than treatment with OSG.     

Persistent organic pollutants in atmospheric deposition and biomonitoring with Tillandsia usneoides (L.) in an industrialized area in Rio de Janeiro state, southeast Brazil--Part II: PCB and PAH

Monitoring of immission of persistent organic pollutants in the industrialized area of Volta Redonda (V.R.) and in the National Park of Itatiaia (PNI) in southeast Brazil was performed using an endemic bromeliad species as biomonitor and measuring bulk deposition rates of polychlorinated biphenyls (PCB) and polycyclic aromatic hydrocarbons (PAH). For the sum of PCB, overall deposition rates were between 17 and 314 ng/(m2 day) in winter and between 43 and 81 ng/(m2 day) in summer, respectively. Deposition rates of dioxin-like PCBs ranged from 0.14 to 2.8 pg WHO-TEQ/(m2 day) in winter and from 0.90 to 4.3 pg WHO-TEQ/(m2 day) in summer. PCB deposition rates (total PCB and WHO-TEQ) were in the same range in winter in V.R. and PNI. In summer, contamination levels in V.R. were 6-10-folds higher than in PNI. PCB concentrations in biomonitor samples from V.R. and PNI were in the same range in summer and in winter. Concentrations of total PCB ranged from 14 to 95 microg/kg dry matter (d.m.) in winter and from 18 to 27 microg/kg d.m. in summer, respectively. The TEQ values were between 1.7 and 4.1 ng WHO-TEQ/kg d.m. in winter and between 1.9 and 2.9 ng WHO-TEQ/kg d.m. in summer. PCB concentrations of di-ortho PCB but not of non-ortho PCB were a factor of 2-4 lower in summer in both areas. PCB congener profiles resembled those from technical formulations. The profiles shifted to the higher chlorinated congeners in summer, probable due to revolatilisation of the lighter components at higher temperatures. PCB profiles in biomonitor resembled those from deposition samples and the shift to the heavier congeners in summer was even more pronounced. PAH deposition rates were in a similar range in both areas (131-2415 ng/(m2 day)). PAH levels in biomonitor samples from V.R. were about one order of magnitude higher than in samples from PNI indicating the impact of local sources. PAH profiles revealed stationary thermal processes as main source of contamination in V.R. whereas in PNI, biomass burning seems to be the main contamination source.     

Exemplifying whole-plant ozone uptake in adult forest trees of contrasting species and site conditions

Whole-tree O3 uptake was exemplified for Picea abies, Fagus sylvatica and Larix decidua in stands at high and low altitude and contrasting water availability through sap flow measurement in tree trunks, intrinsically accounting for drought and boundary layer effects on O3 flux. O3 uptake of evergreen spruce per unit foliage area was enhanced by 100% at high relative to low elevation, whereas deciduous beech and larch showed similar uptake regardless of altitude. The responsiveness of the canopy conductance to water vapor and, as a consequence, O3 uptake to soil moisture and air humidity did not differ between species. Unifying findings at the whole-tree level will promote cause-effect based O3 risk assessment and modeling.