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.     

Decline and diversity in Swedish seas: Environmental narratives in marine history,science and policy

Ambio - Before the mid-twentieth century, there was no comprehensive narrative about empirical conditions in Swedish seas. Around 1970, this view changed profoundly. In line with growing research...     

Understanding interactions between urban development policies and GHG emissions: A case study in Stockholm Region

Human-induced urban growth and sprawl have implications for greenhouse gas (GHG) emissions that may not be included in conventional GHG accounting methods. Improved understanding of this issue requires use of interactive, spatial-explicit social–ecological systems modeling. This paper develops a comprehensive approach to modeling GHG emissions from urban developments, considering Stockholm County, Sweden as a case study. GHG projections to 2040 with a social–ecological system model yield overall greater emissions than simple extrapolations in official climate action planning. The most pronounced difference in emissions (39% higher) from energy use single-residence buildings resulting from urban sprawl. And this difference is not accounted for in the simple extrapolations. Scenario results indicate that a zoning policy, restricting urban development in certain areas, can mitigate 72% of the total emission effects of the model-projected urban sprawl. The study outcomes include a decision support interface for communicating results and policy implications with policymakers.

     

Correction to: Keeping pace with forestry: Multi-scale conservation in a changing production forest matrix

Ambio - In the original published article, the sentence “Nevertheless, semi-natural forest remnants continue to be harvested and fragmented (Svensson et al. 2018; Jonsson et al. 2019), and...     

The tox is in the detail: technical fundamentals for designing,performing, and interpreting experiments on toxicity of microplastics and associated substances

Over the last 10 years, there has been a plethora of experimental studies estimating the potential of microplastic particles (MPs) to exert toxic effects in the environment, many specifically focusing on their postulated capacity to enhance the transfer of environmental pollutants into organisms after ingestion. Obviously, there is little to no consensus on appropriate experimental design, which is mainly owing to the novelty, the interdisciplinarity of the subject, and the complexity of parameters involved. This results in fundamental discrepancies regarding the materials applied, the approach for spiking MPs with pollutants, and the exact exposure scenario. Aiming for a non-chemist audience and providing illustrative, representative, and comparative examples, this review first outlines the theoretical essentials of processes involved in sorption. Also, it discusses the implications for designing experimental approaches using MPs and interpreting the results obtained under consideration of their relevance for environmental conditions. It may help to improve the interpretation of studies on MP toxicity already published, while also calling experimenters’ attention to various aspects important to consider when designing and performing environmentally relevant experiments with MPs.

     

The dual discourse of urban resilience: robust city and self-organised neighbourhoods

Resilience has become a dominant disaster governance discourse. It has been criticised for insufficiently addressing systemic vulnerabilities while urging the vulnerable to self-organise. The urban resilience discourse involves a particular disconnect: it evokes ‘robustness’ and unaffectedness at the city scale on the one hand, and self-organisation of disaster-affected people and neighbourhoods on the other. This paper explains and illustrates the dual discourse through a case study on the reconstruction of informal and low-income settlements in the aftermath of the fire in Valparaíso, Chile, in 2014, focusing on the communication contents of two non-governmental organisations (NGOs). These NGOs deployed the discourse differently, yet both called for affected neighbourhoods to build a more robust city through self-organisation, and both suggested their work as the missing link between self-organisation and robustness. A danger in deploying the dual discourse is that it requires people who live in informal and low-income settlements to earn their right to the robust city through ‘better’ self-organisation based on fragmented visions.     

New Metal Emission Patterns in Road Traffic Environments

The increased awareness of traffic as a major diffuse metal emission source emphasizes the need for more detailed information on the various traffic-related sources and how and where the metals are dispersed. In this study, metal emission patterns in the road traffic environment were examined from the perspective of different surrounding factors, e.g. the importance of intersections, deceleration, vehicle speed and traffic density. A total of 148 topsoil samples from 18 south Swedish roads were analysed (using GFAAS) for traffic-emitted metals, i.e. Cd, Cr, Cu, Ni, Pb, Sb and Zn. The roadside topsoil metal concentrations were used to examine correlations between metals and surrounding factors. The studied metals were divided into three groups corresponding to different emission sources: metals from decelerating activities (Cu, Sb and Zn), metals as historical residues from the combustion of petrol (Pb and Cd), and non-source-specific metals (Cr and Ni). It was found that Cu and Sb, despite their rather short history as traffic-emitted metals, have increased more than eightfold in roadside soils compared to background levels. The major source of road traffic related Cu and Sb is brake linings. The significant increase of Cu and Sb in roadside topsoil stresses the need for metal transport studies as well as effect studies of these metals. Metals emitted due to decelerating activities were not correlated to elevated concentrations near road junctions. Emission patterns of traffic-related metals alongside roads are crucial in order to be able to evaluate the optimal localization of storm water treatment ponds.