Shared signals -'alarm calls' from plants increase apparency to herbivores and their enemies in nature

The attraction of natural enemies of herbivores by volatile organic compounds as an induced indirect defence has been studied in several plant systems. The evidence for their defensive function originates mainly from laboratory studies with trained parasitoids and predators; the defensive function of these emissions for plants in natural settings has been rarely demonstrated. In native populations and laboratory Y-tube choice experiments with transgenic Nicotiana attenuata plants unable to release particular volatiles, we demonstrate that predatory bugs use terpenoids and green leaf volatiles (GLVs) to locate their prey on herbivore-attacked plants. By attracting predators with volatile signals, this native plant reduces its herbivore load – demonstrating the defensive function of herbivore-induced volatile emissions. However, plants producing GLVs are also damaged more by flea beetles. The implications of these conflicting ecological effects for the evolution of induced volatile emissions and for the development of sustainable agricultural practices are discussed.     

Interactive Effects Between Reindeer and Habitat Fertility Drive Soil Nutrient Availabilities in Arctic Tundra

Herbivores impact nutrient availability and cycling, and the net effect of herbivory on soil nutrients is generally assumed to be positive in nutrient-rich environments and negative in nutrient-poor ones. This is, however, far from a uniform pattern, and there is a recognized need to investigate any interactive effects of herbivory and habitat fertility (i.e., plant C/N ratios) on soil nutrient availabilities. We determined long-term effects of reindeer on soil extractable nitrogen (N) and phosphorus (P) and their net mineralization rates along a fertility gradient of plant carbon (C) to N and P ratios in arctic tundra. Our results showed that reindeer had a positive effect on soil N in the more nutrient-poor sites and a negative effect on soil P in the more nutrient-rich sites, which contrasts from the general consensus. The increase in N availability was linked to a decrease in plant and litter C/N ratios, suggesting that a shift in vegetation composition toward more graminoids favors higher N cycling. Soil P availability was not as closely linked to the vegetation and is likely regulated more by herbivore-induced changes in soil physical and chemical properties. The changes in soil extractable N and P resulted in higher soil N/P ratios, suggesting that reindeer could drive the vegetation toward P-limitation. This research highlights the importance of including both the elements N and P and conducting studies along environmental gradients in order to better understand the interactive effects of herbivory and habitat fertility on nutrient cycling and primary production.     

Protein Engineering Allows for Mild Affinity-based Elution of Therapeutic Antibodies

Presented here is an engineered protein domain, based on Protein A, that displays a calcium-dependent binding to antibodies. This protein, Z_Ca, is shown to efficiently function as an affinity ligand for mild purification of antibodies through elution with ethylenediaminetetraacetic acid. Antibodies are commonly used tools in the area of biological sciences and as therapeutics, and the most commonly used approach for antibody purification is based on Protein A using acidic elution. Although this affinity-based method is robust and efficient, the requirement for low pH elution can be detrimental to the protein being purified. By introducing a calcium-binding loop in the Protein A-derived Z domain, it has been re-engineered to provide efficient antibody purification under mild conditions. Through comprehensive analyses of the domain as well as the Z_Ca–Fc complex, the features of this domain are well understood. This novel protein domain provides a very valuable tool for effective and gentle antibody and Fc-fusion protein purification.     

Trampling and Spatial Heterogeneity Explain Decomposer Abundances in a Sub-Arctic Grassland Subjected to Simulated Reindeer Grazing

Mammal grazing is composed of three mechanisms—removal of foliar tissue (defoliation), return of nutrients via dung and urine (fertilization), and trampling. To evaluate the relative role of these mechanisms in the effect of reindeer grazing on soil biota in northern grasslands, we subjected experimental plots in a sub-arctic alpine meadow to defoliation, fertilization (using NPK-solution), simulated trampling, and their factorial combinations once a year from 2002 to 2004 and measured the response of plants and decomposers (including microbes, nematodes, collembolans, and enchytraeids) in 2004. Trampling affected both plant and decomposer communities: the coverage of the moss Pleurozium schreberi and the sedge Carex vaginata, as well as the abundance of collembolans and enchytraeids were reduced in trampled plots. Trampling and fertilization also interacted significantly, with fertilization increasing the abundance of bacteria and bacterial-feeding and omnivorous nematodes in trampled plots only, and trampling decreasing fungal biomass in non-fertilized plots only. Defoliation had no overall effects on plants or decomposers. Nematode genera were not affected by the experimental treatments, but nematode and plant communities were significantly associated, and all decomposer biota, except collembolans, were strongly affected by the spatial heterogeneity of the study site. Our results indicate that trampling may have larger and defoliation and fertilization smaller roles than anticipated in explaining reindeer grazing effects in sub-arctic grasslands. However, even the effects of trampling seem to be outweighed by the spatial heterogeneity of decomposer abundances. This suggests that in sub-arctic grasslands spatial variation in abiotic factors can be a more important factor than grazing in controlling soil biota abundances. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Author contributions  LIS was involved in planning of the study, fieldwork, lab work, analysis, and wrote the article with contributions from all other authors; JM and MMK conceived the study and contributed to the data analyses; MMK further contributed to the field work and JM refined the final appearance of the text; JO started and was responsible for managing the field experiment, collecting the plant data and gave advice on statistical analysis.     

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas

Human blood plasma can be obtained relatively noninvasively and contains proteins from most, if not all, tissues of the body. Therefore, an extensive, quantitative catalog of plasma proteins is an important starting point for the discovery of disease biomarkers. In 2005, we showed that different proteomics measurements using different sample preparation and analysis techniques identify significantly different sets of proteins, and that a comprehensive plasma proteome can be compiled only by combining data from many different experiments. Applying advanced computational methods developed for the analysis and integration of very large and diverse data sets generated by tandem MS measurements of tryptic peptides, we have now compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high-confidence sets. It includes a hierarchy of protein identifications at different levels of redundancy following a clearly defined scheme, which we propose as a standard that can be applied to any proteomics data set to facilitate cross-proteome analyses. Further, to aid in development of blood-based diagnostics using techniques such as selected reaction monitoring, we provide a rough estimate of protein concentrations using spectral counting. We identified 20,433 distinct peptides, from which we inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%. We have made this resource available via PeptideAtlas, a large, multiorganism, publicly accessible compendium of peptides identified in tandem MS experiments conducted by laboratories around the world.     

Fermentation characteristics of Dekkera bruxellensis strains

The influence of pH, temperature and carbon source (glucose and maltose) on growth rate and ethanol yield of Dekkera bruxellensis was investigated using a full-factorial design. Growth rate and ethanol yield were lower on maltose than on glucose. In controlled oxygen-limited batch cultivations, the ethanol yield of the different combinations varied from 0.42 to 0.45 g (g glucose)⁻¹ and growth rates varied from 0.037 to 0.050 h⁻¹. The effect of temperature on growth rate and ethanol yield was negligible. It was not possible to model neither growth rate nor ethanol yield from the full-factorial design, as only marginal differences were observed in the conditions tested. When comparing three D. bruxellensis strains and two industrial isolates of Saccharomyces cerevisiae, S. cerevisiae grew five times faster, but the ethanol yields were 0–13% lower. The glycerol yields of S. cerevisiae strains were up to six-fold higher compared to D. bruxellensis, and the biomass yields reached only 72–84% of D. bruxellensis. Our results demonstrate that D. bruxellensis is robust to large changes in pH and temperature and may have a more energy-efficient metabolism under oxygen limitation than S. cerevisiae.