Energetically relevant predator–prey body mass ratios and their relationship with predator body size

Food web structure and dynamics depend on relationships between body sizes of predators and their prey. Species‐based and community‐wide estimates of preferred and realized predator–prey mass ratios (PPMR) are required inputs to size‐based size spectrum models of marine communities, food webs, and ecosystems. Here, we clarify differences between PPMR definitions in different size spectrum models, in particular differences between PPMR measurements weighting prey abundance in individual predators by biomass (r^bio) and numbers (r^num). We argue that the former weighting generates PPMR as usually conceptualized in equilibrium (static) size spectrum models while the latter usually applies to dynamic models. We use diet information from 170,689 individuals of 34 species of fish in Alaskan marine ecosystems to calculate both PPMR metrics. Using hierarchical models, we examine how explained variance in these metrics changed with predator body size, predator taxonomic resolution, and spatial resolution. In the hierarchical analysis, variance in both metrics emerged primarily at the species level and substantially less variance was associated with other (higher) taxonomic levels or with spatial resolution. This suggests that changes in species composition are the main drivers of community‐wide mean PPMR. At all levels of analysis, relationships between weighted mean r^bio or weighted mean r^num and predator mass tended to be dome‐shaped. Weighted mean r^num values, for species and community‐wide, were approximately an order of magnitude higher than weighted mean r^bio, reflecting the consistent numeric dominance of small prey in predator diets. As well as increasing understanding of the drivers of variation in PPMR and providing estimates of PPMR in the north Pacific Ocean, our results demonstrate that that r^bio or r^num, as well as their corresponding weighted means for any defined group of predators, are not directly substitutable. When developing equilibrium size‐based models based on bulk energy flux or comparing PPMR estimates derived from the relationship between body mass and trophic level with those based on diet analysis, weighted mean r^bio is a more appropriate measure of PPMR. When calibrating preference PPMR in dynamic size spectrum models then weighted mean r^num will be a more appropriate measure of PPMR.     

MarVis: a tool for clustering and visualization of metabolic biomarkers

Background

Gene set analysis based on Gene Ontology (GO) can be a promising method for the analysis of differential expression patterns. However, current studies that focus on individual GO terms have limited analytical power, because the complex structure of GO introduces strong dependencies among the terms, and some genes that are annotated to a GO term cannot be found by statistically significant enrichment.

Results

We proposed a method for enriching clustered GO terms based on semantic similarity, namely cluster enrichment analysis based on GO (CeaGO), to extend the individual term analysis method. Using an Affymetrix HGU95aV2 chip dataset with simulated gene sets, we illustrated that CeaGO was sensitive enough to detect moderate expression changes. When compared to parent-based individual term analysis methods, the results showed that CeaGO may provide more accurate differentiation of gene expression results. When used with two acute leukemia (ALL and ALL/AML) microarray expression datasets, CeaGO correctly identified specifically enriched GO groups that were overlooked by other individual test methods.

Conclusion

By applying CeaGO to both simulated and real microarray data, we showed that this approach could enhance the interpretation of microarray experiments. CeaGO is currently available at http://chgc.sh.cn/en/software/CeaGO/.     

Southern African Biological Soil Crusts are Ubiquitous and Highly Diverse in Drylands,Being Restricted by Rainfall Frequency

Biological soil crusts (BSCs) are found in all dryland regions of the world, including the polar regions. They are also known to occur in the southern African region. Although there were a number of case studies on BSCs from that region, we did not know if they are a normal part of the vegetation cover or just a phenomenon that occasionally occurs here and there. In order to investigate diversity, distribution patterns, and the driving factors of both, we followed a random sampling system of observatories along a transect, stretching from the Namibian-Angolan border down south to the Cape Peninsula, covering seven different major biomes. Biological soil crusts were found to occur in six out of seven biomes. Despite the fact that soil-dwelling algae occurred in the Fynbos biome, crust formation was not observed for hitherto unknown reasons. Seven BSC types were distinguished on the basis of morphology and taxonomic composition: three of them were cyanobacteria-dominated, one with additional chlorolichens, two with bryophytes, one hypolithic type restricted to quartz gravel pavements, and the unique lichen fields of the Namib Desert. Besides 29 green algal species in 21 genera, one heterokont alga, 12 cyanolichens, 14 chlorolichens, two genera of liverworts, and three genera of mosses, these crusts are positioned among the most diverse BSCs worldwide mainly because of the unusual high cyanobacterial species richness comprising 58 species in 21 genera. They contribute considerably to the biodiversity of arid and semi-arid bioregions. Taxonomic diversity of cyanobacteria was significantly higher in the winter rain zone than in the summer rain zone (54 versus 32 species). The soil photosynthetic biomass (chlorophylla/m2), the carbon content of the soil and the number of BSC types were significantly higher in the winter rain zone (U27, 29=215.0, p=0.004 [chla]; U21, 21=135.0, p=0.031 [C]; U27, 29=261.5, p=0.028 [BSC types]; excluding the fog-dominated Namib biome). The winter rain zone is characterized by a lower precipitation amount, but a higher rain frequency with the number of rainy days more evenly distributed over the year. The dry period is significantly shorter per year in the winter rain zone (U8, 9=5.0, p=0.003). We conclude that rain frequency and duration of dry periods rather than the precipitation amount is the main factor for BSC growth and succession. Nitrogen content of the soils along the transect was generally very low and correlated with soil carbon content. There was a weak trend that an increasing proportion of silt and clay (<0.63 mm) in the soil is associated with higher values of BSC chlorophyll content (Pearson correlation coefficient=0.314, p=0.237). Furthermore, we found a significant positive correlation between silt and clay and the number of BSC types (Pearson correlation coefficient=0.519, p=0.039), suggesting that fine grain-size promotes BSC succession and their biomass content. Lichens and bryophytes occurred in BSCs with lower disturbance frequencies (e.g. trampling) only. Crust thickness and chlorophyll content increased significantly from crusts of the early successional type to the late successional crust types. From our results, we conclude that BSCs are a normal and frequent element of the vegetation in arid and semi-arid southwestern Africa, and that rain frequency and duration of dry periods rather than the precipitation amount are the key factors for the development, differentiation and composition of BSCs.     

The dopamine-D2-receptor agonist ropinirole dose-dependently blocks the Ca2+-triggered permeability transition of mitochondria

Ropinirole, an agonist of the post-synaptic dopamine D2-receptor, exerts neuroprotective activity. The mechanism is still under discussion. Assuming that this neuroprotection might be associated with inhibition of the apoptotic cascade underlying cell death, we examined a possible effect of ropinirole on the permeability transition pore (mtPTP) in the mitochondrial inner membrane. Using isolated rat liver mitochondria, the effect of ropinirole was studied on Ca²⁺-triggered large amplitude swelling, membrane depolarization and cytochrome c release. In addition, the effect of ropinirole on oxidation of added, membrane-impermeable NADH was investigated. The results revealed doubtlessly, that ropinirole can inhibit permeability transition. In patch-clamp experiments on mitoplasts, we show directly that ropinirole interacts with the mtPTP. Thus, ropinirole reversibly inhibits the opening of mtPTP with an IC₅₀ of 3.4 µM and a Hill coefficient of 1.3. In both systems (i.e. energized mitochondria and mitoplasts) the inhibitory effect on permeability transition was attenuated by increasing concentrations of inorganic phosphate. In addition, we showed with antimycin A-treated mitochondria that ropinirole failed to suppress respiratory chain-linked reactive oxygen species release. In conclusion, our data suggest that the neuroprotective activity of ropinirole is due to the blockade of the Ca²⁺-triggered permeability transition.     

Assessment of the skin irritation potential of chemicals by using the SkinEthic reconstructed human epidermal model and the common skin irritation protocol evaluated in the ECVAM skin irritation validation study

Currently, two reconstructed human skin models, EpiDerm and EPISKIN are being evaluated in an ECVAM skin irritation validation study. A common skin irritation protocol has been developed, differing only in minor technical details for the two models. A small-scale study, applying this common skin irritation protocol to the SkinEthic reconstructed human epidermis (RHE), was performed at ZEBET at the BfR, Berlin, Germany, to consider whether this protocol could be successfully transferred to another epidermal model. Twenty substances from Phase III of the ECVAM prevalidation study on skin irritation were tested with the SkinEthic RHE. After minor, model-specific adaptations for the SkinEthic RHE, almost identical results to those obtained with the EpiDerm and EPISKIN models were achieved. The overall accuracy of the method was more than 80%, indicating a reliable prediction of the skin irritation potential of the tested chemicals when compared to in vivo rabbit data. As a next step, inter laboratory reproducibility was assessed in a study conducted between ZEBET and the Department of Experimental Toxicology, Schering AG, Berlin, Germany. Six coded substances were tested in both laboratories, with three different batches of the SkinEthic model. The assay results showed good reproducibility and correct predictions of the skin irritation potential for all six test chemicals. The results obtained with the SkinEthic RHE and the common protocol were reproducible in both phases, and the overall outcome is very similar to that of earlier studies with the EPISKIN and EpiDerm models. Therefore, the SkinEthic skin irritation assay test protocol can now be evaluated in a formal "catch-up" validation study.     

Immunocytochemical localization of the prostaglandin-forming cyclooxygenase in the cerebellar cortex

An indirect immunocytofluorescence technique was used to examine the distribution of the prostaglandin-forming cyclooxygenase in the cerebellar cortex of the pig, guinea pig, rat, mouse, cow, rabbit and sheep. Cyclooxygenase antigenicity was detected (a) in the cell bodies of Bergman glial cells in the Purkinje cell layer of the porcine, ovine and bovine cerebellar cortex; (b) in small arterioles throughout the cerebellar cortex in the sheep and cow; and (c) in the endothelial cells of large arteries in all the species examined. No cyclooxygenase-positive staining was apparent in neuronal cell bodies of granule, basket, stellate or Purkinje cells. Our results establish that prostaglandin endoperoxides can be synthesized by the arterial vasculature and at least certain glial cells in the central nervous system.