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.     

An in vitro/in vivo screening assay as a sensitive tool to assess endocrine disruptive activity in surface water

Adult male fathead minnow were exposed for 14 or 28-days under flow-through conditions to undiluted filtered water samples from the rivers Meuse and Rhine in the Netherlands. The experiment included two vessels per treatment each containing 10 fish and samples of five fish were taken after 14 and 28 days. Additional groups were exposed to 17alpha-ethinylestradiol (EE2) as a reference and untreated drinking water as a negative control. Major endpoints examined included induction of vitellogenin (VTG) synthesis, VTG mRNA activity, hepato- and gonadosomatic indices (HSI and GSI) and gonadal histology. No significant difference was recorded in body weight or mean GSI values between the various treatments. Only exposure to Meuse water resulted in significantly higher HSI means after 14 days. Histological examination showed no apparent effects on gonadal tissue except for eosinophilic blood plasma in fish exposed to Meuse water or EE2. After 14 and 28 days, elevated VTG and VTG mRNA levels were measured in most livers of the fish exposed to Meuse water, but not in the fish exposed to Rhine water. This was confirmed by measuring estrogenic responses in the in vitro ER CALUX assay. Induction of VTG synthesis proved to be the most sensitive endpoint in the Non Spawning Male Fish Assay for in vivo detection of bio-available estrogenic activity supplementary to a sensitive in vitro assay. The other endpoints examined varied too much and required a higher number of fish or replicates to achieve sufficient power for statistical testing making them less animal friendly.     

Effect of vegetation type on throughfall deposition and seepage flux

This paper compares different vegetation types (coniferous and deciduous forest, grassed and pure heathland) in terms of input (throughfall deposition) and output (seepage flux) in a region with intermediate nitrogen load (+/-20kg Nha(-1)y(-1) via bulk precipitation) in comparable conditions in north Belgium. Coniferous forest (two plots Pinus sylvestris and two plots Pinus nigra) received significantly higher nitrogen and sulphur throughfall deposition than deciduous forest and heathland. Grassed and pure heathland had significantly highest throughfall quantities of Ca(2+) and Mg(2+), respectively. The observed differences in throughfall deposition between the different vegetation types were not univocally reflected in the ion seepage flux. Considerable seepage fluxes of NO(3)(-), SO(4)(2-), Ca(2+) and Al(III) were only found under the P. nigra plots. We discuss our hypothesis that the P. nigra forests already evolved to a situation of N saturation, while the other vegetation types did not.     

Comparison of vehicle activity and emission inventory between Beijing and Shanghai

Vehicle emission inventory is a critical element for air quality study. This study created systemic methods to establish a vehicle emission inventory in Chinese cities. The methods were used to obtain credible results of vehicle activity in Beijing and Shanghai. On the basis of the vehicle activity data, the International Vehicle Emission model is used to establish vehicle emission inventories. The emissions analysis indicates that 3 t of particulate matter (PM), 199 t of nitrogen oxides (NO(x)), 192 t of volatile organic compounds (VOCs), and 2403 t of carbon monoxide (CO) are emitted from on-road vehicles each day in Beijing, whereas 4 t of PM, 189 t of NO(x), 113 t of VOCs, and 1009 t of CO are emitted in Shanghai. Although common features were found in these two cities (many new passenger cars and a high taxi proportion in the fleet), the emission results are dissimilar because of the different local policy regarding vehicles. The method to quantify vehicle emission on an urban scale can be applied to other Chinese cities. Also, knowing how different policies can lead to diverse emissions is beneficial knowledge for other city governments.     

Refinery evaluation of optical imaging to locate fugitive emissions

Fugitive emissions account for approximately 50% of total hydrocarbon emissions from process plants. Federal and state regulations aiming at controlling these emissions require refineries and petrochemical plants in the United States to implement a Leak Detection and Repair Program (LDAR). The current regulatory work practice, U.S. Environment Protection Agency Method 21, requires designated components to be monitored individually at regular intervals. The annual costs of these LDAR programs in a typical refinery can exceed US$1,000,000. Previous studies have shown that a majority of controllable fugitive emissions come from a very small fraction of components. The Smart LDAR program aims to find cost-effective methods to monitor and reduce emissions from these large leakers. Optical gas imaging has been identified as one such technology that can help achieve this objective. This paper discusses a refinery evaluation of an instrument based on backscatter absorption gas imaging technology. This portable camera allows an operator to scan components more quickly and image gas leaks in real time. During the evaluation, the instrument was able to identify leaking components that were the source of 97% of the total mass emissions from leaks detected. More than 27,000 components were monitored. This was achieved in far less time than it would have taken using Method 21. In addition, the instrument was able to find leaks from components that are not required to be monitored by the current LDAR regulations. The technology principles and the parameters that affect instrument performance are also discussed in the paper.     

Effect of chelating agents and solubility of cadmium complexes on uptake from soil by Brassica juncea

Brassica juncea, or Indian mustard, was grown in soil artificially contaminated with either a soluble salt, CdCl(2), at 186mg Cdkg(-1), or alternately an insoluble, basic salt, CdCO(3), at 90mg Cdkg(-1). These experiments study the range of Cd uptake by Indian mustard from conditions of very high Cd concentration in a soluble form to the other extreme with an insoluble Cd salt. After plants were established, four different chelating agents were applied. Chelating agents increased plant uptake of Cd from the CdCl(2) soil but did not significantly increase plant uptake of Cd from the CdCO(3) contaminated soil. Addition of ethylenediaminetetraacetic acid (EDTA) increased the plant concentration of Cd by almost 10-fold in soils contaminated with CdCl(2), with a concentration of 1283mg Cdkg(-1) in the dried EDTA-treated plants over a concentration of 131mg Cdkg(-1) in plants without added chelate. However, EDTA increased the aqueous solubility of Cd by 36 times over the soil matrix without added chelator, and thereby, increased the possibility of leaching. Other chelators used in both experiments were ethylenebis(oxyethylenenitrilo)tetraacetic acid, trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid, and diethylenetriaminepentaacetic acid (DTPA) increasing Cd in plants to 1240, 962, and 437mg Cdkg(-1), respectively. The other chelating agents increased the solubility of Cd in the leachate but not to the extent of EDTA. Comparing all chelating agents studied, DTPA increased plant uptake in terms of Cd in dried plant concentration most relative to the solubility of complexed Cd in runoff water.     

Differential responses of the freshwater wetland species Juncus effusus L. and Caltha palustris L. to iron supply in sulfidic environments

Sulfur pollution can lead to serious problems in freshwater wetlands, including phosphorus eutrophication and sulfide toxicity. We tested the effects of anaerobic iron-rich groundwater discharge in fens, simulated by iron injection, on two characteristic species (Juncus effusus and Caltha palustris) in a sulfidic environment. Biomass production of C. palustris roots showed an optimum response to the combined addition of iron and sulfide, with highest values at intermediate concentrations of both substances. Iron deficiency apparently occurred at low iron concentrations, while at high iron concentrations, growth was decreased. For J. effusus, in contrast, no toxic effects were found of both iron and sulfide. This could be explained by larger radial oxygen loss (ROL) of J. effusus and could not be explained by differences in phosphorous concentrations. The results of our experiments confirm that iron-rich groundwater discharge has the potential to affect vegetation composition through toxicity modification in sulfidic environments.     

Assimilation efficiencies of Cd and Zn in the common carp (Cyprinus carpio): effects of metal concentration, temperature and prey type

The impact of several factors on the assimilation efficiency (AE) of Cd and Zn from food in the common carp (Cyprinus carpio) was studied. Tested prey species were midge larvae (Chironomus riparius), zebra mussels (Dreissena polymorpha) and oligochaetes (Tubifex tubifex). The Cd load of the larvae did not affect the Cd AE in the carp. The Zn AE however, was negatively related to the Zn load of the prey. Food quantity and starvation of the carp did not significantly affect the Cd AE. For Zn, a significant decrease in AE was found when carp were fed ad libitum. Decreasing the temperature from 25 degrees C to 15 degrees C did not influence the Cd AE, while for Zn a significant decrease of the AE was measured. Carp assimilated Cd from both zebra mussels and oligochaetes with a significantly lower efficiency in comparison to the midge larvae, although Zn AEs was prey independent.     

Fully Bio-Sourced Nylon 11/Raw Lignin Composites: Thermal and Mechanical Performances

Ecofriendly fully bio-composites based on polyamide 11 (PA11) and lignin have been prepared on the entire concentration range using a twin-screw extruder. In this work, PA11 was blended with lignin by direct extrusion technology without any chemical pre- or in-situ- modifications or physical pretreatments. The presence of various organic and inorganic impurities in the selected technical lignin have been maintained. The incorporation of this cheap renewable material from biomass in bio-based PA11 was inspected by an array of characterization tools. Also, the effect of the presence of lignin on the morphology and on the mechanical properties of the resulting materials was examined. Finally, in-situ investigation of structural evolution in PA11 induced by the presence of lignin was analyzed by Fast Scanning Chip Calorimetry.