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.     

Intra-cultivar variability of the soil-to-grain transfer of fallout 137Cs and 90Sr for winter wheat

Differences between the root uptake of fallout radionuclides by different cultivars ('inter-cultivar' variability) growing on the same field may be influenced not only by genetic differences of the cultivars, but also by the spatial variability of the soil-to-grain transfer within the cultivation area of each cultivar. This 'intra-cultivar' variability was investigated in 2001 and 2002 for 137Cs and 90Sr using three winter wheat cultivars with four replicates for each cultivar at three different sites in Bavaria, Germany. The intra-cultivar variability proved to be in the same range as the inter-cultivar variability which was determined earlier at the same sites for both radionuclides. An ANOVA of the 137Cs data set revealed that the variability of the 137Cs soil-to-grain transfer was caused by the soil and climate (year) at the field sites and the interaction of cultivar and field. A significant contribution of the factor 'cultivar' alone to the variability could not be detected. This may be due to the complex environmental conditions to which plants are exposed in field experiments. To find wheat cultivars with minimal uptake of fallout radionuclides it may be better to examine the molecular mechanisms of their root uptake in order to identify targets for breeding "safer" plants.     

Flood monitoring in a semi-arid environment using spatially high resolution radar and optical data

The geographic term "Niger Inland Delta" stands for a vast plain of approximately 40,000 km(2), which is situated in the western Sahel (Republic of Mali). The Inland Delta is affected by yearly inundation through the variable water levels of the Niger-Bani river system. Due to a good availability of (surface) water, the ecosystem at the Niger Inland Delta serves as resting place stop-over for many migrating birds and other wildlife species as well as economic base for farmers and pastoral people. To foster the sustainable usage of its natural resources and to protect this natural heritage, the entire Niger Inland Delta became RAMSAR site in 2004. This paper aims to test to which extent texture analysis can improve the quality of flood monitoring in a semi-arid environment using spatially high resolution ASAR imaging mode data. We found the Gray Level Dependence Method (GLDM) was most suitable proceeding for our data. Several statistical parameters were calculated via co-occurrence matrices and were used to classify the images in different gradation of soil moisture classes. In a second step we used additional information from spatially high resolution optical data (ASTER) to improve the separability of open water areas from moisture/vegetated areas.     

Daytime resolved analysis of polycyclic aromatic hydrocarbons in urban aerosol samples - impact of sources and meteorological conditions

Urban aerosol was collected in a summer and a winter campaign for 7 and 3 days, respectively. Low volume samples were taken with a time resolution of 160 min using a filter/sorption cartridge system extended by an ozone scrubber. Concentrations of mainly particle associated polycyclic aromatic hydrocarbons (PAH) and oxidised PAH (O-PAH) were determined by gas chromatography/high resolution mass spectrometry. The sampling site was located in the city centre of Augsburg, Germany, near major roads with high traffic volume. The daily concentrations and profiles were mainly governed by local emissions from traffic and domestic heating, as well as by the meteorological conditions. During the winter campaign, concentrations were more than 10 fold higher than during the summer campaign. Highest concentrations were found concurrent with low boundary layer heights and low wind speeds. Significant diurnal variation of the PAH profiles was observed. Enhanced influences of traffic related PAH on the PAH profiles were evident during daytime in summer, whereas emissions from hot water generation and domestic heating were obvious during the night time of both seasons. A general idea about the global meteorological situation was acquired using back trajectory calculations (NOAA ARL HYSPLIT4). Due to high local emissions in combination with low air exchange during the two sampling campaigns, effects of mesoscale transport were not clearly observable.     

Long-term change in drivers of forest cover expansion: an analysis for Switzerland (1850-2000)

Regional Environmental Change - The spatial distribution of forests in Europe represents the legacy of centuries of human land use decisions. Due to the limited availability of historical data,...     

Comparison of micrometeorological and two-film estimates of air–water gas exchange for alpha-hexachlorocyclohexane in the Canadian archipelago

The air-sea gas exchange of alpha-hexachlorocyclohexane (α-HCH) in the Canadian Arctic was estimated using a micrometeorological approach and the commonly used Whitman two-film model. Concurrent shipboard measurements of α-HCH in air at two heights (1 and 15 m) and in surface seawater were conducted during the Circumpolar Flaw Lead study in 2008. Sampling was carried out during eight events in the early summer time when open water was encountered. The micrometeorological technique employed the vertical gradient in air concentration and the wind speed to estimate the flux; results were corrected for atmospheric stability using the Monin-Obukhov stability parameter. The Whitman two-film model used the concentrations of α-HCH in surface seawater, in bulk air at 1 and 15 m above the surface, and the Henry's law constant adjusted for temperature and salinity to derive the flux. Both approaches showed that the overall net flux of α-HCH was from water to air. Mean fluxes calculated using the micrometeorological technique ranged from -3.5 to 18 ng m(-2) day(-1) (mean 7.4), compared to 3.5 to 14 ng m(-2) day(-1) (mean 7.5) using the Whitman two-film model. Flux estimates for individual events agreed in direction and within a factor of two in magnitude for six of eight events. For two events, fluxes estimated by micrometeorology were zero or negative, while fluxes estimated with the two-film model were positive, and the reasons for these discrepancies are unclear. Improvements are needed to shorten air sampling times to ensure that stationarity of meteorological conditions is not compromised over the measurement periods. The micrometeorological technique could be particularly useful to estimate fluxes of organic chemicals over water in situations where no water samples are available.     

Remote sampling of a CO2 point source in an urban setting

High frequency CO₂ and wind speed measurements were used to examine the urban baseline eddy covariance CO₂ flux and analyse the CO₂ rich plume from a local power station. A reliable relationship between high frequency CO₂ maxima and the rate of CO₂ emission at the power station was established. This relationship was shown to be highly dependant on wind speed. The ensemble mean plume was found to be Gaussian in horizontal profile with a width dependant on wind speed. The relationship between peak CO₂ mixing ratio and averaging time was shown to be a simple power law with a time exponent of approximately 0.5. The large, short pulses in CO₂ mixing ratio in the power plant plume were found to have an approximately Lorentzian shape. These pulses generated negative vertical eddy flux measurements so data from the plume sector were necessarily excluded from the flux baseline results. The plume-excluded flux had a similar magnitude and variability to those reported in other urban CO₂ flux studies despite this site not being ideal due to the proximity of roughness elements to the measurement point.     

Misuse of null hypothesis significance testing: would estimation of positive and negative predictive values improve certainty of chemical risk assessment?

Although generally misunderstood, the p value is the probability of the test results or more extreme results given H₀ is true: it is not the probability of H₀ being true given the results. To obtain directly useful insight about H₀, the positive predictive value (PPV) and the negative predictive value (NPV) may be useful extensions of null hypothesis significance testing (NHST). They provide information about the probability of statistically significant and non-significant test outcomes being true based on an a priori defined biologically meaningful effect size. The present study explores the utility of PPV and NPV in an ecotoxicological context by using the frequently applied Daphnia magna reproduction test (OECD guideline 211) and the chemical stressor lindane as a model system. The results indicate that especially the NPV deviates meaningfully between a test design strictly following the guideline and an experimental procedure controlling for α and β at the level of 0.05. Consequently, PPV and NPV may be useful supplements to NHST that inform the researcher about the level of confidence warranted by both statistically significant and non-significant test results. This approach also reinforces the value of considering α, β, and a biologically meaningful effect size a priori.