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.     

Body mass estimations for <Emphasis Type="Italic">Plateosaurus engelhardti</Emphasis> using laser scanning and 3D reconstruction methods

Both body mass and surface area are factors determining the essence of any living organism. This should also hold true for an extinct organism such as a dinosaur. The present report discusses the use of a new 3D laser scanner method to establish body masses and surface areas of an Asian elephant (Zoological Museum of Copenhagen, Denmark) and of Plateosaurus engelhardti, a prosauropod from the Upper Triassic, exhibited at the Paleontological Museum in Tübingen (Germany). This method was used to study the effect that slight changes in body shape had on body mass for P. engelhardti. It was established that body volumes varied between 0.79 m³ (slim version) and 1.14 m³ (robust version), resulting in a presumable body mass of 630 and 912 kg, respectively. The total body surface areas ranged between 8.8 and 10.2 m², of which, in both reconstructions of P. engelhardti, ∼33% account for the thorax area alone. The main difference between the two models is in the tail and hind limb reconstruction. The tail of the slim version has a surface area of 1.98 m², whereas that of the robust version has a surface area of 2.73 m². The body volumes calculated for the slim version were as follows: head 0.006 m³, neck 0.016 m³, fore limbs 0.020 m³, hind limbs 0.08 m³, thoracic cavity 0.533 m³, and tail 0.136 m³. For the robust model, the following volumes were established: 0.01 m³ head, neck 0.026 m³, fore limbs 0.025 m³, hind limbs 0.18 m³, thoracic cavity 0.616 m³, and finally, tail 0.28 m³. Based on these body volumes, scaling equations were used to assess the size that the organs of this extinct dinosaur have.     

Synthesis of polyhydroxyalkanoates in municipal wastewater treatment.

Biologically derived polyesters known as polyhydroxyalkanoates (PHAs) represent a potentially "sustainable" replacement to fossil-fuel-based thermoplastics. However, current commercial practices that produce PHA with pure microbial cultures grown on renewable, but refined, feedstocks (i.e., glucose) under sterile conditions do not represent a sustainable commodity. Here, we report on PHA production with a mixed microbial consortium indigenous to an activated sludge process on carbon present in municipal wastewaters. Reactors operated under anaerobic/aerobic and aerobic-only mode and fed primary solids fermenter liquor maintained a mixed microbial consortium capable of synthesizing PHA at 10 to 25% (w/w), while reducing soluble COD by approximately 62 to 71%. More critically, an aerobic batch reactor seeded from the anaerobic/aerobic reactor and fed fermenter liquor achieved approximately 53% PHA (w/w). Results presented suggest that environmentally benign production of biodegradable polymers is feasible. We further used PHA-rich biomass to produce a natural fiber-reinforced thermoplastic composite that can be used to offset advanced wastewater treatment costs.     

Investigations on mechanical biological treatment of waste in South America: towards more sustainable MSW management strategies

This work presents an analysis on the suitability of mechanical biological treatment of municipal solid waste in South America, based on two previous experimental investigations carried out in two different countries. The first experiment was performed for determining the mass and volume reduction of MSW in the province of Concepción (Chile). The implemented bench-scale process consisted of a manual classification and separation stage, followed by an in-vessel biological degradation process. The second experiment consisted of a full-scale experiment performed in the city of Estrela (Brazil), where the existing municipal waste management facility was adapted to enhance the materials sorting and separation. Expressed in wet weight composition, 85.5% of the material input in the first experiment was separated for biological degradation. After 27 days of processing, 60% of the initial mass was reduced through degradation and water evaporation. The final fraction destined for landfilling equals 59% of the total input mass, corresponding to about 50% of the initial volume. In the second experiment, the fraction destined to landfill reaches 46.6% of the total input waste mass, whilst also significantly reducing the total volume to be disposed. These results, and the possible recovery of material streams suitable for recycling or for preparing solid recovered fuels, are the main advantages of the studied process.     

Fine-grain spatial patterning and dynamics of land use and agrobiodiversity amid global changes in the Bolivian Andes

Our research addresses the gap in scientific research on the fine-grain spatial patterns and social–ecological interactions of land use and agrobiodiversity. The spatial dimension of agrobiodiversity dynamics potentially strengthens the social–ecological resilience and food security of smallholders by buffering risk and vulnerability. Our research integrates the scientific theories, concepts, and methods of spatial externalities, social–ecological interactions, geospatial land and global change sciences, and political ecology. We designed a case study of the Arbieto-Tarata landscape in the Bolivian Andes that comprises a globally significant agrobiodiversity hot spot of Andean maize. The Arbieto-Tarata landscape, which contains nearly 8000 fields at 2500–2800 masl, is representative of mixed-use smallholder agri-food systems amid global changes. Our research predicts spatial spillover and edge effects of combined social and environmental factors leading to the clustering of same-crop fields. Findings reveal significant levels of the predicted clustering between 2006 and 2012. The degree of this clustering is found to differ among geographic and environmental sub-areas reflecting fine-grain variation of local causal linkages. Extra-local causal linkages include high levels of migration, water resource shortages, and urbanization. Results show the influences of informal and formal coordination in the spatial clustering of same-crop fields. This field-level coordination improves the efficiency of resource allocations and lowers costs of production. It enables the viability of high-agrobiodiversity Andean maize in smallholder land use and agri-food systems amid global changes. The article discusses the broader policy and scientific implications of these findings including scaling up and support of the social–ecological resilience of agrobiodiversity globally.     

Fall fertilization timing effects on nitrate leaching and turfgrass color and growth

Fall season fertilization is a widely recommended practice for turfgrass. Fertilizer applied in the fall, however, may be subject to substantial leaching losses. A field study was conducted in Connecticut to determine the timing effects of fall fertilization on nitrate N (NO3-N) leaching, turf color, shoot density, and root mass of a 90% Kentucky bluegrass (Poa pratensis L.), 10% creeping red fescue (Festuca rubra L.) lawn. Treatments consisted of the date of fall fertilization: 15 September, 15 October, 15 November, 15 December, or control which received no fall fertilizer. Percolate water was collected weekly with soil monolith lysimeters. Mean log(10) NO3-N concentrations in percolate were higher for fall fertilized treatments than for the control. Mean NO3-N mass collected in percolate water was linearly related to the date of fertilizer application, with higher NO3-N loss for later application dates. Applying fall fertilizer improved turf color and density but there were no differences in color or density among applications made between 15 October and 15 December. These findings suggest that the current recommendation of applying N in mid- to late November in southern New England may not be compatible with water quality goals.     

Spatiotemporal evolution of soil pH and zinc after the Aznalcollar mine spill

The residual pollution after the Aznalcóllar (southwestern Spain) pyrite mine spill is still a threat due to the continuing oxidation of sulfuric minerals. The objective of this paper was to analyze the combined effect of pyrite oxidation, sugar beet foam applications, and meteorological conditions on the spatiotemporal evolution of the pH and EDTA-extractable Zn concentration, using non co-located data from 11 sampling dates between June 1999 and March 2002. Median pH values ranged from 4.4 at the beginning of the monitoring period to 7.6 at the end, although values near 2.5 were observed throughout the entire period, despite of two sugar beet foam (SBF) applications. Zinc distributions were positively skewed and median concentrations ranged from 17 to 94 mg kg(-1). The inverse relationship between pH and Zn became weaker toward the end of the monitoring period as a consequence of the precipitation and posterior dissolution of newly formed minerals from the reaction products of the pyrite oxidation. Normal score maps showed that after the SBF applications only 0.5% of the monitored area was below the pH = 4 threshold, while on other dates up to one-third of the area remained below this value. The better performance of the second SBF application could be explained in terms of pyrite oxidation pathways and environmental conditions. From this analysis, with data obtained under uncontrolled field conditions, it is concluded that SBF should be applied before or during the wet and cold season to alleviate acidification, caused by the oxidation of pyrite or other sulfuric minerals.     

TUGAI: An Integrated Simulation Tool for Ecological Assessment of Alternative Water Management Strategies in a Degraded River Delta

The development of ecologically sound water allocation strategies that account for the needs of riverine ecosystems is a pressing issue, especially in semiarid river basins. In the Aral Sea Basin, a search for strategies to mitigate ecological and socioeconomic deterioration has been in process since the early 1990s. The Geographic Information System–based simulation tool TUGAI has been developed to support the policy determination process by providing a simple, problem-oriented method to assess ecological effects of alternative water management strategies for the Amudarya River. It combines a multiobjective water allocation model with simple, spatially explicit statistical and rule-based models of landscape dynamics. Changes in environmental conditions are evaluated by a fuzzy habitat suitability index for Populus euphratica, which is the dominant species of the characteristic riverine Tugai forests. Water management scenarios can be developed by altering spatiotemporal water distribution in the delta area or the amount of water inflow into the delta. Outcomes of scenario analysis are qualitative comparisons of the ecological effects of different options for a time period of up to 28 years. The given approach utilizes different types of knowledge, from quantitative hydrological data to qualitative local expert knowledge. The main purpose of the tool is to integrate the knowledge in a comprehensive way to make it available for discussions on alternative policies in moderated workshops with stakeholders. In this article, the modules of the tool, their integration, and three hypothetical scenarios are presented. Based on the experience gained when developing the TUGAI tool, we propose that the general framework can be transferred to other areas where tradeoffs in water allocation between the environment and other water users are of major concern. The potential for a simulation tool to structure and inform a complex resource management situation by involving local experts and stakeholders in the development of possible future scenarios will become increasingly valuable for transparent and participatory resource management.