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.     

Population structure and historical demography of the thorny skate (<Emphasis Type="Italic">Amblyraja radiata</Emphasis>, Rajidae) in the North Atlantic

Population genetic structure of the thorny skate (Amblyraja radiata) was surveyed in >300 individuals sampled from Newfoundland, Iceland, Norway, the Kattegat and the central North Sea. A 290-bp fragment of the mt cytochrome-b gene was first screened by SSCP. Sequences of SSCP haplotypes revealed 34 haplotypes, 14 of which were unique to Iceland, 3 to Newfoundland, 1 to Norway and 3 to the Kattegat. The global F _ST was weak but significant. Removal of the two Kattegat locations, which were the most differentiated, resulted in no significant genetic differentiation. Haplotype diversity was high and evenly distributed across the entire Atlantic (h = 0.8) with the exception of the North Sea (h = 0.48). Statistical parsimony revealed a star-like genealogy with a central widespread haplotype. A subsequent nested clade analysis led to the inference of contiguous expansion with evidence for long distance dispersal between Newfoundland and Iceland. Historical demographic analysis showed that thorny skates have undergone exponential population expansion that started between 1.1 million and 690,000 years ago; and that the Last Glacial Maximum apparently had little effect. These results strongly differ from those of a parallel study of the thornback ray (Raja clavata) in which clear structure and former refugial areas could be identified. Although both species have similar life history traits and overlapping ranges, the continental shelf edge apparently does not present a barrier to migration in A. radiata, as it does for R. clavata.     

Feeding aggregations of sea stars (<Emphasis Type="Italic">Asterias</Emphasis> spp. and <Emphasis Type="Italic">Henricia sanguinolenta</Emphasis>) associated with sea urchin (<Emphasis Type="Italic">Strongylocentrotus droebachiensis</Emphasis>) grazing fronts in Nova Scotia

Migrating feeding aggregations (or fronts) of sea urchins can dramatically alter subtidal seascapes by destructively grazing macrophytes. While direct effects of urchin fronts on macrophytes (particularly kelps) are well documented, indirect effects on associated fauna are largely unknown. Secondary aggregations of predators and scavengers form around fronts of Strongylocentrotus droebachiensis in Nova Scotia. We recorded mean densities of the sea stars Asterias spp. (mainly A. rubens) and Henricia sanguinolenta of up to 11.6 and 1.7 individuals 0.25 m⁻² along an urchin front over 1 year. For Asterias, mean density at the front was 7 and 15 times greater than in the kelp bed and adjacent barrens, respectively. There was strong concordance between locations of peak density of urchins and sea stars (Asterias r = 0.98; H. sanguinolenta r = 0.97) along transects across the kelp–barrens interface, indicating that sea star aggregations migrated along with the urchin front at rates of up to 2.5 m per month. Size–frequency distributions suggest that Asterias at the front were drawn from both the barrens (smaller individuals) and the kelp bed (larger individuals). These sea stars fed intensively on mussels on kelp holdfasts and in adjacent patches. Urchin grazing may precipitate aggregations of sea stars and other predators or scavengers by incidentally consuming or damaging mussels and other small invertebrates, and thereby releasing a strong odor cue. Consumption of protective holdfasts and turf algae by urchins could facilitate feeding by these consumers, which may obtain a substantial energy subsidy during destructive grazing events.     

The clean development mechanism and community forests in Sub-Saharan Africa: reconsidering Kyoto’s “moral position” on biocarbon sinks in the carbon market

Negotiations of the Kyoto Protocol reached what has been called a moral position on biocarbon sinks which saw important limitations on their use in the Clean Development Mechanism (CDM), the Protocol’s main carbon offset system. After outlining this moral position, this article examines the consequences of these limitations on the viability of community forest participation in the CDM through a case study of three community forests in West Africa. Results suggest that there is significant carbon mitigation potential from forest conservation, reforestation as well as from improved fuelwood cookstoves at the community level. Yet under the current rules of the CDM, little of this overall carbon mitigation potential is able to be realized. Using qualitative research methodologies, it was learned that community respondents showed a pragmatic, yet cautious interest in the CDM while also emphasizing a need for land-use flexibility. The paper closes with a political discussion of the “‘moral position” on biocarbon sinks in the carbon market and concludes with policy recommendations for biocarbon sinks, in both the CDM and REDD, in the post-Kyoto climate change regime.     

Observations and analytical modeling of freshwater and rainwater lenses in coastal dune systems

Observations are reported on (i) groundwater recharge rates under various types of vegetation as measured with megalysimeters in the dunes, (ii) freshwater lenses along the Dutch North Sea coast in the early 1900s, and (iii) rainwater lenses that develop on top of laterally migrating, artificially recharged riverwater. Subsequently analytical methods are presented to estimate annual natural groundwater recharge as function of rainfall and vegetation, and to calculate the size, shape and transition zone of freshwater lenses on saline groundwater and rainwater lenses on infiltrated riverwater. An empirical correction factor, based on the hydraulic resistance of an aquitard within the freshwater lens, is proposed to account for the frequently observed reduction of the Ghyben-Herzberg ratio of 40. This factor raises the groundwater table, reduces the depth of the fresh/salt interface and increases the lens formation time. The suite of methods offers a tool box for knowledge based water management of dune systems, by rapidly predicting: (i) more or less autonomous changes due to sealevel rise, climate change and vegetation development; and (ii) the potential (side) effects of interventions. Knowing what happened or will happen to the fresh water lens or a rainwater lens is important, because changes impact on important natural habitat parameters such as salinity, depth to groundwater table, decalcification rate (and thus on pH, Ca/Al, PO₄, NH₄) and nutrient availability, and on drinking water supply. The analytical models are applied to predict effects of sealevel rise, coastal progradation, vegetation changes, and increased temperature of coastal air and river water to be infiltrated.     

Long-term passive restoration following fluvial deposition of sulphidic copper tailings: nature filters out the solutions

Despite the growing popularity of ecological restoration approach, data on primary succession on toxic post-mining substrates, under site environmental conditions which considerably differ from the surrounding environment, are still scarce. Here, we studied the spontaneous vegetation development on an unusual locality created by long-term and large-scale fluvial deposition of sulphidic tailings from a copper mine in a pronouncedly xerothermic, calcareous surrounding. We performed multivariate analyses of soil samples (20 physical and chemical parameters) and vegetation samples (floristic and structural parameters in three types of occurring forests), collected along the pollution gradients throughout the affected floodplain. The nature can cope with two types of imposed constraints: (a) excessive Cu concentrations and (b) very low pH, combined with nutrient deficiency. The former will still allow convergence to the original vegetation, while the latter will result in novel, depauperate assemblages of species typical for cooler and moister climate. Our results for the first time demonstrate that with the increasing severity of environmental filtering, the relative importance of the surrounding vegetation for primary succession strongly decreases.     

Differential responses in American (<Emphasis Type="Italic">Castanea dentata</Emphasis> Marshall) and Chinese (<Emphasis Type="Italic">C. mollissima</Emphasis> Blume) chestnut (Falales: Fagaceae) to foliar application of jasmonic acid

Summary.  Tannins are plant defense compounds that exhibit antibiotic (e.g. toxic) and antixenotic (e.g. repellent) effects against an array of plant pests. They are broadly divided into two major groups, hydrolysable tannins (gallotannins and ellagitannins) and proanthocyanidins, each with an undetermined number of compounds. We investigated constitutive levels of hydrolysable tannins and proanthocyanidins in the leaves and stems of American (Castanea dentata Marshall) (Fagales: Fagaceae) and Chinese (C. mollissima Blume) chestnut. American chestnut contained more proanthocyanidins in leaves and stems than Chinese chestnut, but Chinese chestnut contained more foliar hydrolysable tannins. Regardless of these differences, gypsy moth (Lymantria dispar L, Lepidoptera: Lymantriidae) performance did not differ when fed American and Chinese chestnuts. We also investigated the effects of jasmonic acid (JA) treatment on differential tannin induction in American and Chinese chestnut leaves and stems. JA treatment increased proanthocyanidins in American chestnut stems and hydrolysable tannins in both tissue types of American chestnut, but did not influence tannin concentrations in Chinese chestnut leaves or stems. HPLC-ESI-MS analysis of pooled samples suggested that hydrolysable tannins in each tissue were qualitatively comprised primarily of ellagitannins, and JA generally increased the number of hydrolysable tannins that could be detected by ESI-MS. Third, we investigated the performance of gypsy moths on JA treated and untreated American and Chinese chestnut. Caterpillar relative growth was not influenced by JA treatment on Chinese chestnut, but decreased in response to JA application on American chestnut. Our results indicate that JA-dependent defenses differ between these chestnut species. This study improves our understanding of ecologically important differences in tannin induction and herbivore susceptibility in Castanea, and has important implications in efforts for American chestnut restoration and commercial chestnut production.     

Cache and carry: hoarding behavior of arctic fox

Food-hoarding animals are expected to preferentially cache items with lower perishability and/or higher consumption time. We observed arctic foxes (Alopex lagopus) foraging in a greater snow goose (Anser caerulescens atlanticus) colony where the main prey of foxes consisted of goose eggs, goslings, and lemmings (Lemmus and Dicrostonyx spp.). We recorded the number of prey consumed and cached and the time that foxes invested in these activities. Foxes took more time to consume a goose egg than a lemming or gosling but cached a greater proportion of eggs than the other prey type. This may be caused by the eggshell, which presumably decreases the perishability and/or pilfering risk of cached eggs, but also increases egg consumption time. Arctic foxes usually recached goose eggs but rarely recached goslings or lemmings. We tested whether the rapid-sequestering hypothesis could explain this recaching behavior. According to this hypothesis, arctic foxes may adopt a two-stage strategy allowing both to maximize egg acquisition rate in an undefended nest and subsequently secure eggs in potentially safer sites. Foxes spent more time carrying an egg and traveled greater distances when establishing a secondary than a primary cache. To gain further information on the location and subsequent fate of cached eggs, we used dummy eggs containing radio transmitters. Lifespan of primary caches increased with distance from the goose nest. Secondary caches were generally located farther from the nest and had a longer lifespan than primary caches. Behavioral observations and the radio-tagged egg technique both gave results supporting the rapid-sequestering hypothesis.     

Filtering effect of wind flow turbulence on atmospheric pollutant dispersion

This paper presents a model for coupling the statistics of wind velocity distribution and atmospheric pollutant dispersion. The effect of wind velocity distribution is modeled as a three-dimensional finite-impulse response (3D-FIR) filter. A phase space representation of the 3D-FIR filter window is discussed. The resulting pollutant dispersion is the multiplication in the phase space of the 3-D Fourier transform of the pollutant concentration and the volume described by the filter window coefficients. The shape of the filter window in the phase space enables representing such effects as vortex shedding thermal currents, etc. The impact of spatial distribution of the sensors on the resulting pollutant spatial distribution and the 3-D FIR filter model employed also discuss. The case of a neutrally buoyant plume emitted from an elevated point source in a turbulent boundary layer considers. The results show that wind turbulence is an important factor in the pollutant dispersion and introduces expected random fluctuations in pollutant distribution and leads to spreading the distribution due to wind mixing.     

Assessment of heavy metals in the particulate matter of two Brazilian metropolitan areas by using <Emphasis Type="BoldItalic">Tillandsia usneoides</Emphasis> as atmospheric biomonitor

Purpose  

The aims of this paper were to quantify the heavy metals (HM) in the air of different sites in Rio de Janeiro (RJ) and Salvador (SA) using Tillandsia usneoides (Bromeliaceae) as a biomonitor, and to study the morphology and elemental composition of the air particulate matter (PM) retained on the Tillandsia surface.