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.     

Diet of four species of deep-sea isopods (Crustacea: Malacostraca: Peracarida) in the South Atlantic and the Southern Ocean

The food of four species of asellote isopods (Crustacea, Malacostraca), Haploniscus rostratus, Haploniscus unicornis, Acanthocope galatheae and Betamorpha fusiformis, was evaluated by analysis of their gut contents. The isopods were sampled at several stations on the abyssal plains of Guinea Basin, Angola Basin and Cape Basin (southeast Atlantic), the Weddell Sea abyssal plain and the Antarctic continental slope during the DIVA and ANDEEP expeditions in 2000, 2001 and 2005. While all species had mineral particles in their guts and mucus material was the most frequent food item, the remaining gut contents differed among species. Betamorpha fusiformis fed mostly on phytodetritus, especially in the Southern Ocean basins and ingested along with it whole calcareous foraminifers. Acanthocope galatheae showed some differences in gut contents between basins, but in the Guinea Basin, the contents were to a large extent stercomata, i.e., waste pellets of soft-walled foraminifers, i.e., the Komokiaceae. Indications were that the haploniscids were feeding on detritus and agglutinating foraminifers (stercomata). This indicates spatial differences in food availability for this diverse group of deep-sea isopods and the importance of poorly known foraminiferal groups, like the Komokiaceae, as a food source in the deep sea.     

Characterizing sources of nitrate leaching from an irrigated dairy farm in Merced County, California

Dairy farms comprise a complex landscape of groundwater pollution sources. The objective of our work is to develop a method to quantify nitrate leaching to shallow groundwater from different management units at dairy farms. Total nitrate loads are determined by the sequential calibration of a sub-regional scale and a farm-scale three-dimensional groundwater flow and transport model using observations at different spatial scales. These observations include local measurements of groundwater heads and nitrate concentrations in an extensive monitoring well network, providing data at a scale of a few meters and measurements of discharge rates and nitrate concentrations in a tile-drain network, providing data integrated across multiple farms. The various measurement scales are different from the spatial scales of the calibration parameters, which are the recharge and nitrogen leaching rates from individual management units. The calibration procedure offers a conceptual framework for using field measurements at different spatial scales to estimate recharge N concentrations at the management unit scale. It provides a map of spatially varying dairy farming impact on groundwater nitrogen. The method is applied to a dairy farm located in a relatively vulnerable hydrogeologic region in California. Potential sources within the dairy farm are divided into three categories, representing different manure management units: animal exercise yards and feeding areas (corrals), liquid manure holding ponds, and manure irrigated forage fields. Estimated average nitrogen leaching is 872 kg/ha/year, 807 kg/ha/year and 486 kg/ha/year for corrals, ponds and fields respectively. Results are applied to evaluate the accuracy of nitrogen mass balances often used by regulatory agencies to assess groundwater impacts. Calibrated leaching rates compare favorably to field and farm scale nitrogen mass balances. These data and interpretations provide a basis for developing improved management strategies.     

INACTIVATION OF GIARDIA MURIS CYSTS BY CHLORAMINES1

ABSTRACT: In a study to measure the efficacy of chioramines at inactivating Giardia cysts, the ability of cysts to excyst was measured after exposure to different concentrations of chloramines, for different times, and at different temperatures and pH. The chloramines were generated by mixing ammonium sulfate and sodium hypochlorate in water to approximate a 7:1 chlorine:ammonia ratio by weight. Times of 40, 80, 180, and 270 minutes; temperatures of 3, 10, and 18°C; target chioramine concentrations of 0.4, 1.4, 2.0, and 2.6 mg/L; and pH of 7.0 and 8.5 were the actual values tested. The combinations of these variables that were able to inactivate >99.8 percent of the cysts were a minimum chloramine concentration of 2.26 mg/L applied for 270 minutes at a water temperature of 10°C; and at 18°C, averaged minimum chloramine concentrations of 2.14 and 1.55 mg/L applied for 180 and 270 minutes, respectively. The minimum CT values corresponding to these combinations capable of >99.8 percent cyst inactivation, are 610 at 10°C and 385 at 18°C. Temperature was noted to exert a major effect on the ability of chloramines to inactivate cysts. Modifications of the methods used to generate chloramines may have an effect on the capacity of this disinfectant to inactivate cysts.     

Nutrient Uptake in a Large Urban River1

Abstract: Small streams have been shown to be efficient in retaining nutrients and regulating downstream nutrient fluxes, but less is known about nutrient retention in larger rivers. We quantified nutrient uptake length and uptake velocity in a regulated urban river to determine the river’s ability to retain nutrients associated with wastewater treatment plant (WWTP) effluent. We measured net uptake of soluble reactive phosphorus (SRP), dissolved organic phosphorus, ammonium (NH₄), nitrate, and dissolved organic nitrogen in the Chattahoochee River, Atlanta, GA by following the downstream decline of nutrients and fluoride from WWTP effluent on 10 dates under low flow conditions. Uptake of all nutrients was sporadic. On many dates, there was no evidence of measurable nutrient uptake lengths within the reach; indeed, on several dates release of inorganic N and P within the sample reach led to increased nutrient export downstream. When uptake occurred, SRP uptake length was negatively correlated with total suspended solids and temperature. Uptake velocities of SRP and NH₄ in the Chattahoochee River were lower than velocities in less‐modified systems, but they were similar to those measured in other WWTP impacted systems. Lower uptake velocities indicate a diminished capacity for nutrient uptake.     

Health risks of residential wood heat

The resurgence in the use of wood in the United States for residential heating has been accompanied by a dramatic increase in deaths and injuries from residential fires. Toxic materials present in woodsmoke also appear to present a significant public health hazard. As a result of these factors, production of residential wood heat can be up to two orders of magnitude more hazardous than generation of an equivalent amount of electric energy at a coal-fired power plant. Proper care in installation and operation of wood stoves, as well as technological innovations that control wood-stove emissions, can greatly reduce the health and safety hazards of residential heating with wood.     

Mercury in a northeastern Brazilian mangrove area, a case study: potential of the mangrove oyster Crassostrea rhizophorae as bioindicator for mercury

The Channel of Santa Cruz is a mangrove area in northeastern Brasil 40 km north of Recife. Until 1991 a chlor-alkali factory discharged large amounts of mercury into the main tributary of the channel, the Rio Botafogo. The objective of this study was to assess the potential of the mangrove oyster Crassostrea rhizophorae as a bioindicator for mercury in this area and to examine the influence of condition on mercury concentrations in the oysters. The investigation was carried out in the late rainy season (July to September) 1993, in the rainy season (April to June) 1994 and in the dry season (November/December) 1994. At 11 stations in the channel, mangrove oysters, surface sediments and suspended matter were sampled, representing different compartments of the system. The distribution of mercury in the Channel of Santa Cruz exhibited for all compartments the same distinct spatial pattern with maxima in the Rio Botafogo. Seasonal variations were small and revealed no clear tendencies. In addition, mangrove oysters were transplanted from more contaminated stations to less contaminated stations and vice versa. These experiments were designed to study the oysters' capability to adjust their mercury concentrations to a changing bioavailability of mercury. The transplantation experiments suggest that the oysters are capable to adjust to changing ambient mercury availability within a few months. The transplantation experiments also revealed the importance of condition changes on the mercury concentration of the oysters. This factor should not be ignored during pollution studies. However, condition had apparently no strong influence on the spatial or seasonal mercury variations of the oysters. The mangrove oyster is a suitable bioindicator for long-term changes in mercury availability. Received: 20 August 1997 / Accepted: 15 January 1998