Short-term signals of climate change along an altitudinal gradient in the South Alps

Short-term changes in plant species number, frequency and composition were studied along an altitudinal gradient crossing four summits from the treeline ecotone to the subnival zone in the South Alps (Dolomites, Italy). Large-scale (summit areas) and small-scale patterns (16 plots of 1 m2/summit) were monitored. After 5 years, a re-visitation of the summit areas revealed a considerable increase of species richness at the upper alpine and subnival zone (10% and 9%, respectively) and relatively modest increases at the lower alpine zone and the treeline ecotone (3% and 1%, respectively). At the small scale, the results were partly different, with species richness decreasing at the lower summits and increasing at the higher summits. The changes can most likely be attributed to climate warming effects and to competitive interactions. The main newcomers at the lower three summits were species from the treeline and the lower altitudinal zones. Only at the highest summit, the newcomers came from the alpine species pool. At the treeline ecotone, the abundance of Pinus cembra, of dwarf shrubs and clonal graminoid species increased. Here, displacements of alpine species may be predicted for the near future. At the higher summits, expansions of the established alpine species and further invasions of species from lower altitudes are forecasted.     

Combined chemical and enzymatic stable isotope labeling for quantitative profiling of detergent-insoluble membrane proteins isolated using Triton X-100 and Brij-96

Effective quantitative profiling of detergent-insoluble membrane proteins using high-throughput mass spectrometry (MS)-based proteomics would allow a better understanding of physiological and pathological processes that take place at the cell surface. To increase the coverage of proteins present in detergent-resistant membrane microdomains (DRMMs), a combination of 16O/18O and isotope coded affinity tags (ICAT) labeling was used in a comparative analysis of detergent-insoluble membrane proteins isolated from rat basophilic leukemia cells (RBL-2H3), with either Triton X-100 or Brij-96. The analysis resulted in the quantification of 738 unique proteins from Triton X-100 and Brij-96 isolated DRMMs, significantly exceeding the number of proteins quantified from either single labeling technique. Twenty-five noncysteine-containing proteins were quantified, as well as 32 cysteine-containing proteins that would have been missed if either 16O/18O or ICAT labeling had been used exclusively, which illustrate better proteome coverage and enhanced ability to quantitate. The comparative analysis revealed that proteins were more readily extracted using Triton X-100 than Brij-96; however, Triton X-100 also extracted larger quantities of non-DRMMs-associated proteins. This result confirms previous, targeted studies suggesting that DRMMs isolated using Triton X-100 and Brij-96 differ in their protein content.     

A multi-proxy Late-glacial palaeoenvironmental record from Lake Bled, Slovenia

This study investigates the palaeoecological record (δ¹⁸O, δ¹³C, pollen, plant macrofossils, chironomids and cladocera) at Lake Bled (Slovenia) sedimentary core to better understand the response of terrestrial and aquatic ecosystems to Late-glacial climatic fluctuations. The multi-proxy record suggests that in the Oldest Dryas, the landscape around Lake Bled was rather open, presumably because of the cold and dry climate, with a trend towards wetter conditions, as suggested by an increase in tree pollen as well as chironomid and cladocera faunas typical for well-oxygenated water. Climatic warming at the beginning of the Late-glacial Interstadial at ca. 14,800 cal yr BP is suggested by an increase in the δ¹⁸O value, the appearance of Betula and Larix pollen and macrofossils, and a warmth-adapted chironomid fauna. With further warming at ca. 13,800 cal yr BP, broad-leaved tree taxa (Quercus, Tilia, Ulmus), Artemisia, and Picea increase, whereas chironomid data (Cricotopus B) suggest lowering of lake levels. After 12,800 cal yr BP (and throughout the Younger Dryas), the climate was colder and drier, as indicated by lower δ¹⁸O values, decline of trees, increase of microscopic charcoal, xerophytes and littoral chironomids. A warmer climate, together with the spread of broad-leaved tree taxa and a deeper, more productive lake, mark the onset of the Late-glacial/Holocene transition. These results suggest that terrestrial and aquatic ecosystems at Lake Bled were very dynamic and sensitive to Late-glacial climatic fluctuations. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorised users. Guest editors: K. Buczkó, J. Korponai, J. Padisák & S. W. Starratt Palaeolimnological Proxies as Tools of Environmental Reconstruction in Fresh Water     

Inflammation-associated enterotypes,host genotype,cage and inter-individual effects drive gut microbiota variation in common laboratory mice

Background

Murine models are a crucial component of gut microbiome research. Unfortunately, a multitude of genetic backgrounds and experimental setups, together with inter-individual variation, complicates cross-study comparisons and a global understanding of the mouse microbiota landscape. Here, we investigate the variability of the healthy mouse microbiota of five common lab mouse strains using 16S rDNA pyrosequencing.

Results

We find initial evidence for richness-driven, strain-independent murine enterotypes that show a striking resemblance to those in human, and which associate with calprotectin levels, a marker for intestinal inflammation. After enterotype stratification, we find that genetic, caging and inter-individual variation contribute on average 19%, 31.7% and 45.5%, respectively, to the variance in the murine gut microbiota composition. Genetic distance correlates positively to microbiota distance, so that genetically similar strains have more similar microbiota than genetically distant ones. Specific mouse strains are enriched for specific operational taxonomic units and taxonomic groups, while the ''cage effect'' can occur across mouse strain boundaries and is mainly driven by Helicobacter infections.

Conclusions

The detection of enterotypes suggests a common ecological cause, possibly low-grade inflammation that might drive differences among gut microbiota composition in mammals. Furthermore, the observed environmental and genetic effects have important consequences for experimental design in mouse microbiome research.     

Variable temperature effects of Open Top Chambers at polar and alpine sites explained by irradiance and snow depth

Environmental manipulation studies are integral to determining biological consequences of climate warming. Open Top Chambers (OTCs) have been widely used to assess summer warming effects on terrestrial biota, with their effects during other seasons normally being given less attention even though chambers are often deployed year‐round. In addition, their effects on temperature extremes and freeze‐thaw events are poorly documented. To provide robust documentation of the microclimatic influences of OTCs throughout the year, we analysed temperature data from 20 studies distributed across polar and alpine regions. The effects of OTCs on mean temperature showed a large range (?0.9 to 2.1 °C) throughout the year, but did not differ significantly between studies. Increases in mean monthly and diurnal temperature were strongly related (R² = 0.70) with irradiance, indicating that PAR can be used to predict the mean warming effect of OTCs. Deeper snow trapped in OTCs also induced higher temperatures at soil/vegetation level. OTC‐induced changes in the frequency of freeze‐thaw events included an increase in autumn and decreases in spring and summer. Frequency of high‐temperature events in OTCs increased in spring, summer and autumn compared with non‐manipulated control plots. Frequency of low‐temperature events was reduced by deeper snow accumulation and higher mean temperatures. The strong interactions identified between aspects of ambient environmental conditions and effects of OTCs suggest that a detailed knowledge of snow depth, temperature and irradiance levels enables us to predict how OTCs will modify the microclimate at a particular site and season. Such predictive power allows a better mechanistic understanding of observed biotic response to experimental warming studies and for more informed design of future experiments. However, a need remains to quantify OTC effects on water availability and wind speed (affecting, for example, drying rates and water stress) in combination with microclimate measurements at organism level.     

A fully-automatic caudate nucleus segmentation of brain MRI: Application in volumetric analysis of pediatric attention-deficit/hyperactivity disorder

Background

Accurate automatic segmentation of the caudate nucleus in magnetic resonance images (MRI) of the brain is of great interest in the analysis of developmental disorders. Segmentation methods based on a single atlas or on multiple atlases have been shown to suitably localize caudate structure. However, the atlas prior information may not represent the structure of interest correctly. It may therefore be useful to introduce a more flexible technique for accurate segmentations.

Method

We present Cau-dateCut: a new fully-automatic method of segmenting the caudate nucleus in MRI. CaudateCut combines an atlas-based segmentation strategy with the Graph Cut energy-minimization framework. We adapt the Graph Cut model to make it suitable for segmenting small, low-contrast structures, such as the caudate nucleus, by defining new energy function data and boundary potentials. In particular, we exploit information concerning the intensity and geometry, and we add supervised energies based on contextual brain structures. Furthermore, we reinforce boundary detection using a new multi-scale edgeness measure.

Results

We apply the novel CaudateCut method to the segmentation of the caudate nucleus to a new set of 39 pediatric attention-deficit/hyperactivity disorder (ADHD) patients and 40 control children, as well as to a public database of 18 subjects. We evaluate the quality of the segmentation using several volumetric and voxel by voxel measures. Our results show improved performance in terms of segmentation compared to state-of-the-art approaches, obtaining a mean overlap of 80.75%. Moreover, we present a quantitative volumetric analysis of caudate abnormalities in pediatric ADHD, the results of which show strong correlation with expert manual analysis.

Conclusion

CaudateCut generates segmentation results that are comparable to gold-standard segmentations and which are reliable in the analysis of differentiating neuroanatomical abnormalities between healthy controls and pediatric ADHD.     

First Report of Tomato infectious chlorosis virus on Tomato in Bulgaria

Virus‐like chlorotic symptoms were observed on tomato plants, cv. Velocity, grown in a greenhouse, region of Plovdiv. Samples collected from the leaves with interveinal yellowing and with initial interveinal chlorosis were tested for virus presence. Only the samples collected from the upper leaves with slight interveinal chlorosis were positive for Tomato infectious chlorosis virus (TICV) in indirect ELISA. Further, RT‐PCR analysis with specific primers for Tomato chlorosis virus (ToCV) heat shock protein 70, for TICV heat shock protein 70 and for TICV minor capsid protein was positive for TICV in all tested samples. No signals were obtained with primers for ToCV. Phylogenetic analysis showed that the Bulgarian sequence of Hsp70 and a sequence of Greek isolate clustered together having the highest resampling score. Regarding CPm, the Bulgarian isolate was more relevant to the French isolate. The obtained results from phylogenetic analysis supported the idea of a close relationship between the Bulgarian and Greek isolates.     

Differential binding of chlorpromazine to human blood cells: Application of the hygroscopic desorption method

Using a modified hygroscopic desorption method (HDM) the binding of chlorpromazine (CPZ) to human blood cells was investigated in the concentration range from 0.01 to 100 μmol/1. For erythrocytes and ghosts the ratio between cell bound and free drug concentration was constant up to 60 μmol/1 CPZ. Saturable binding, however, was observed for lymphocytes, granulocytes and less pronounced for platelets. In contrast to red cells, CPZ binding to white cells and platelets was strongly dependent on pH. For all blood cells a sharp decrease in binding occurred at drug concentrations higher than 60 μmol/1. This can hardly represent a true saturation of binding sites, since membrane damaging effects occur at these concentrations. Our results suggest that binding of CPZ to erythrocytes represents an interaction at the water-membrane interphase. For the different binding pattern of white cells, the cell organelles, the cytoplasma and the different composition of the membranes might be of importance.     

Meta-analysis of duloxetine vs. pregabalin and gabapentin in the treatment of diabetic peripheral neuropathic pain

Background  

Few direct head-to-head comparisons have been conducted between drugs for the treatment of diabetic peripheral neuropathic pain (DPNP). Approved or recommended drugs in this indication include duloxetine (DLX), pregabalin (PGB), gabapentin (GBP) and amitriptyline (AMT). We conducted an indirect meta-analysis to compare the efficacy and tolerability of DLX with PGB and GBP in DPNP, using placebo as a common comparator.