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.     

Urban mining: hibernating copper stocks in local power grids

Large technical systems serving the everyday needs of people, such as water supply systems, power grids or communication networks, are rich in accumulated metals. Over time, parts of these systems have been taken out of use without the system infrastructure being removed from its original location. Such metal stocks in hibernation thus constitute potential resource reservoirs accessible for recovery. In this paper, obsolete stocks of copper situated in the local power grids of two Swedish cities are quantified. Emphasis is also on economic conditions for extracting such “hibernating” cables. The results show that on a per customer basis, the two power grids contain similar amounts of copper, i.e. 0.04–0.05 tonnes per subscriber. However, the share of the copper stock that is in hibernation differs between the grids. In the larger grid of Gothenburg, almost 20% of the copper accumulated in the grid is no longer in use, while the obsolete share does not exceed 5% in the city of Linköping. For managers of local power grids, recovery of hibernating cables could be beneficial if integrated with other maintenance work on the grid. At the present price of copper, however, separate recovery of obsolete cables is not economically justified.     

Fine Particle (PM25) Measurement Methodology,Quality Assurance Procedures,and Pilot Results of the EXPOLIS Study

ABSTRACT

EXPOLIS is a European multicenter (Athens, Basel, Grenoble, Helsinki, Milan, and Prague) air pollution exposure study. It is the first international, population-based, large-scale study, where personal exposures to PM_{2 5} aerosol particles (together with volatile organic compounds and carbon monoxide) are being monitored. EXPOLIS is performed in six different centers across Europe, the sampled aerosol concentrations vary greatly, and the mi-croenvironmental samples are not collected with the same equipment as the personal samples. Therefore careful equipment selection, methods development and testing, and thorough quality assurance and quality control (QA & QC) procedures are essential for producing reliable and comparable PM_2.5 data. This paper introduces the equipment, the laboratory test results, the pilot results, the standard operating procedures, and the QA & QC procedures of EXPOLIS. Test results show good comparability and repeatability between personal and microenvironmen-tal monitors for PM2.5 at different concentration levels measured across Europe in EXPOLIS centers.     

A Field Intercomparison and Fundamental Characterization of Various Dust Samplers with a Reference Sampler

The European Economic Community Council Directive 80/779/EEC¹ describes air quality limit values and guide values for sulfur dioxide and suspended particulates. However, article 10, paragraph 1 does not define well enough the reference method required, amongst others, for the gravimetric measurement of suspended particulates. It is explicity stated in article 10, paragraph 5 of the directive, that “the commission shall, in selected locations in the member states and in cooperation with the latter, carry out studies on the sampling…of suspended particulates. These studies shall be designed in particular to promote the harmonization of methods of sampling and analysis of these pollutants.” Therefore, in a joint research program the Umweltbundesamt (grant #104 02263), the commission of European Communities (grant #84-B-6642-11-017-11-N) and the U.S. EPA (grant #2-43211-3580) funded the development of a reference dust sampler by the Fraunhofer-lnstitute of Toxicology and Aerosol Research (FhITA, in Hannover, Federal Republic of Germany) in order: ? to study the particle size distribution of ambient air aerosol at a number of selected sites;

? to compare the results obtained with the reference dust sampler with those of particle samplers operated in Europe and the United States;

? to verify the applicability of wind tunnel results to sampling behaviour in the free atmosphere.

     

Sperm competition affects sex allocation but not sperm morphology in a flatworm

Sperm competition has been shown to be an important evolutionary agent affecting the behaviour, physiology, and morphology of both males and females. One morphological trait that is particularly likely to be affected by sperm competition is sperm size because it is thought to influence the competitiveness of sperm by determining sperm longevity, motility, and/or their ability to displace competing sperm. Most comparative studies across taxa have found a positive relationship between the level of sperm competition and sperm length, but very few studies have tested for a phenotypically plastic adjustment of sperm morphology in response to sperm competition. In this study, we experimentally tested for an effect of sperm competition on phenotypic plasticity in sperm morphology in an obligately outcrossing simultaneous hermaphrodite, the free-living flatworm Macrostomum lignano, by either raising worms in monogamous pairs (no sperm competition) or in promiscuous groups (intense sperm competition). Worms in groups produced larger testes and smaller ovaries as predicted by sex allocation theory and as previously documented in this species. However, we found no evidence for an effect of group size on sperm morphology, measured as total sperm length, sperm body length, and the length of two different sperm appendages. We conclude that M. lignano may either be incapable of adjusting the sperm morphology in a phenotypically plastic way and/or that there might be no benefit of phenotypic plasticity in sperm traits in this species.     

Distribution,fate and formation of non-extractable residues of a nonylphenol isomer in soil with special emphasis on soil derived organo-clay complexes

Anthropogenic contaminants like nonylphenols (NP) are added to soil, for instance if sewage-sludge is used as fertilizer in agriculture. A commercial mixture of NP consists of more than 20 isomers. For our study, we used one of the predominate isomers of NP mixtures, 4-(3,5-dimethylhept-3-yl)phenol, as a representative compound. The aim was to investigate the fate and distribution of the isomer within soil and soil derived organo-clay complexes. Therefore, ¹⁴C- and ¹³C-labeled NP was added to soil samples and incubated up to 180 days. Mineralization was measured and soil samples were fractionated into sand, silt and clay; the clay fraction was further separated in humic acids, fulvic acids and humin. The organo-clay complexes pre-incubated for 90 or 180 days were re-incubated with fresh soil for 180 days, to study the potential of re-mobilization of incorporated residues. The predominate incorporation sites of the nonylphenol isomer in soil were the organo-clay complexes. After 180 days of incubation, 22 % of the applied ¹⁴C was mineralized. The bioavailable, water extractable portion was low (9 % of applied ¹⁴C) and remained constant during the entire incubation period, which could be explained by an incorporation/release equilibrium. Separation of organo-clay complexes, after extraction with solvents to release weakly incorporated, bioaccessible portions, showed that non-extractable residues (NER) were preferentially located in the humic acid fraction, which was regarded as an effect of the chemical composition of this fraction. Generally, 27 % of applied ¹⁴C was incorporated into organo-clay complexes as NER, whereas 9 % of applied ¹⁴C was bioaccessible after 180 days of incubation. The re-mobilization experiments showed on the one hand, a decrease of the bioavailability of the nonylphenol residues due to stronger incorporation, when the pre-incubation period was increased from 90 to 180 days. On the other hand, a shift of these residues from the clay fraction to other soil fractions was observed, implying a dynamic behavior of incorporated residues, which may result in bioaccessibility of the NER of nonylphenol.     

Educating the next generation of atmospheric scientists within a European Network of Excellence

In order to promote the next generation of atmospheric scientists, the task Training and Education (T&E) in ACCENT, the European Network of Excellence in Atmospheric Composition Change (www.accent-network.org) has developed and implemented an Integrated Learning Environment (ILE). For school teachers and their students, the Internet-based “Global Change Magazine” provides up-to-date and freely accessible scientific material in English and five other languages. Additionally, T&E has produced online teaching material for early-career scientists. These e-learning modules are now being used in University Master's courses across Europe. T&E also organised training events for early-career scientists, combining scientific content with development in transferable skills, to focus on interdisciplinary collaboration, interaction with senior scientists, communication with stakeholders, and dissemination to the general public. Evaluation based on participant feedback evidences the effectiveness of these events, e.g., in terms of motivation to remain in the field. Methodologies and materials from T&E are being published in a Handbook on Best Practice, intended for both educators and scientists around the globe who are involved in education in the field of air quality and climate change science.