Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., two novel anaerobic alkaliphilic species isolated from the serpentinite-hosted Prony Bay Hydrothermal Field (New Caledonia)

Two novel anaerobic alkaliphilic strains, designated as LacT^T and LacV^T, were isolated from the Prony Bay Hydrothermal Field (PBHF, New Caledonia). Cells were motile, Gram-positive, terminal endospore-forming rods, displaying a straight to curved morphology during the exponential phase. Strains LacT^T and LacV^T were mesophilic (optimum 30 °C), moderately alkaliphilic (optimum pH 8.2 and 8.7, respectively) and halotolerant (optimum 2% and 2.5% NaCl, respectively). Both strains were able to ferment yeast extract, peptone and casamino acids, but only strain LacT^T could use sugars (glucose, maltose and sucrose). Both strains disproportionated crotonate into acetate and butyrate. Phylogenetic analysis revealed that strains LacT^T and LacV^T shared 96.4% 16S rRNA gene sequence identity and were most closely related to A. peptidifermentans Z-7036, A. namsaraevii X-07-2 and A. hydrothermalis FatMR1 (95.7%–96.3%). Their genome size was of 3.29 Mb for strain LacT^T and 3.06 Mb for strain LacV^T with a G + C content of 36.0 and 33.9 mol%, respectively. The ANI value between both strains was 73.2 %. Finally, strains LacT^T (=DSM 100337 = JCM 30643) and LacV^T (=DSM 100017 = JCM 30644) are proposed as two novel species of the genus Alkaliphilus, order Clostridiales, phylum Firmicutes, Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., respectively. The genomes of the three Alkaliphilus species isolated from PBHF were consistently detected in the PBHF chimney metagenomes, although at very low abundance, but not significantly in the metagenomes of other serpentinizing systems (marine or terrestrial) worldwide, suggesting they represent indigenous members of the PBHF microbial ecosystem.     

Mapping our knowledge on birds of prey population genetics

Conservation Genetics - The current and rapid anthropogenic environmental changes could disproportionately impact ecosystems, particularly when they affect species with critical roles in ecosystem...     

Proteasome inhibition improves diaphragm function in an animal model for COPD

Diaphragm muscle weakness in patients with chronic obstructive pulmonary disease (COPD) is associated with increased morbidity and mortality. Recent studies indicate that increased contractile protein degradation by the proteasome contributes to diaphragm weakness in patients with COPD. The aim of the present study was to investigate the effect of proteasome inhibition on diaphragm function and contractile protein concentration in an animal model for COPD. Elastase-induced emphysema in hamsters was used as an animal model for COPD; normal hamsters served as controls. Animals were either treated with the proteasome inhibitor Bortezomib (iv) or its vehicle saline. Nine months after induction of emphysema, specific force-generating capacity of diaphragm bundles was measured. Proteolytic activity of the proteasome was assayed spectrofluorometrically. Protein concentrations of proteasome, myosin, and actin were measured by means of Western blotting. Proteasome activity and concentration were significantly higher in the diaphragm of emphysematous hamsters than in normal hamsters. Bortezomib treatment reduced proteasome activity in the diaphragm of emphysematous and normal hamsters. Specific force-generating capacity and myosin concentration of the diaphragm were reduced by ~25% in emphysematous hamsters compared with normal hamsters. Bortezomib treatment of emphysematous hamsters significantly increased diaphragm-specific force-generating capacity and completely restored myosin concentration. Actin concentration was not affected by emphysema, nor by bortezomib treatment. We conclude that treatment with a proteasome inhibitor improves contractile function of the diaphragm in emphysematous hamsters through restoration of myosin concentration. These findings implicate that the proteasome is a potential target of pharmacological intervention on diaphragm weakness in COPD.     

Effects of sheep grazing and temporal variability on population dynamics of the clonal herb <Emphasis Type="Italic">Geranium sylvaticum</Emphasis> in an alpine habitat

An improved understanding of population-level consequences of grazing on plants can be facilitated by an assessment of grazing effects on all stages in the life-cycle. In this study, 6 years of demographic data for three populations of the perennial herb Geranium sylvaticum were analysed. We examined the effects of sheep grazing (high sheep density, low sheep density and no sheep) and interannual climatic variability on vital rates and population growth rates (λ). Grazing did not affect survival or flowering rates, but reduced rates of growth and increased rates of clonal reproduction. At the population level, high contributions from retrogression and clonal reproduction buffered reduced rates of growth and stasis, and no consistent differences in λ between populations exposed to different sheep densities were found. Instead, large between-year variability in λ, independent of sheep density, was detected, related to variation in the local summer climate. The results indicated, however, that grazing effects on λ were more severe in unfavourable than in normal years. Our study highlights that increased clonal reproduction rates functioned as a tolerance mechanism towards grazing in this herb, which forms a mechanism to explain how moderate population responses to grazing in some herbs can arise.     

Reporter gene HEK 293 cells and WNT/Frizzled fusion proteins as tools to study WNT signaling pathways

WNT/Frizzled receptor (FZD) signaling pathways are pivotal for physiological and pathophysiological processes. In humans, the complexity of WNT/FZD signaling is based on 19 WNTs, 10 FZDs and at least two (co)receptors (LRP5/6) mediating supposably four different signaling cascades. The detailed investigation of the specific function of the different initiating components is primarily hampered by the lack of most WNT proteins in a purified form. Therefore, we constructed and examined a chimeric protein of WNT3a and FZD4 as a suitable approach to overcome this obstacle for future studies of the specificity of other WNT/FZD combinations. Furthermore, we produced four different reporter HEK 293 cell lines to quantify the induced activation of the proposed signaling cascades, the β-catenin-, the NFAT-, the AP-1- and the CRE-regulated pathways. The chimera WNT3aFZD4 efficiently induced β-catenin-mediated luciferase activity. This activity was increased 40-fold compared with basal when LRP6 was stably cotransfected, proving that the chimera WNT3aFZD4 can also interact efficiently with LRP6. Our results demonstrate that the approach of using reporter gene cell lines in combination with WNT/FZD chimeras is efficient to study the β-catenin-mediated pathway and should also allow clarifying the specificity of WNT/FZD combinations in the activation of the other pathways.     

IL-4 and IL-13 exposure during mucociliary differentiation of bronchial epithelial cells increases antimicrobial activity and expression of antimicrobial peptides

The airway epithelium forms a barrier against infection but also produces antimicrobial peptides (AMPs) and other inflammatory mediators to activate the immune system. It has been shown that in allergic disorders, Th2 cytokines may hamper the antimicrobial activity of the epithelium. However, the presence of Th2 cytokines also affects the composition of the epithelial layer which may alter its function. Therefore, we investigated whether exposure of human primary bronchial epithelial cells (PBEC) to Th2 cytokines during mucociliary differentiation affects expression of the human cathelicidin antimicrobial protein (hCAP18)/LL-37 and human beta defensins (hBD), and antimicrobial activity.PBEC were cultured at an air-liquid interface (ALI) for two weeks in the presence of various concentrations of IL-4 or IL-13. Changes in differentiation and in expression of various AMPs and the antimicrobial proteinase inhibitors secretory leukocyte protease inhibitor (SLPI) and elafin were investigated as well as antimicrobial activity.IL-4 and IL-13 increased mRNA expression of hCAP18/LL-37 and hBD-2. Dot blot analysis also showed an increase in hCAP18/LL-37 protein in apical washes of IL-4-treated ALI cultures, whereas Western Blot analysis showed expression of a protein of approximately 4.5 kDa in basal medium of IL-4-treated cultures. Using sandwich ELISA we found that also hBD-2 in apical washes was increased by both IL-4 and IL-13. SLPI and elafin levels were not affected by IL-4 or IL-13 at the mRNA or protein level. Apical wash obtained from IL-4- and IL-13-treated cultures displayed increased antimicrobial activity against Pseudomonas aeruginosa compared to medium-treated cultures. In addition, differentiation in the presence of Th2 cytokines resulted in increased MUC5AC production as has been shown previously.These data suggest that prolonged exposure to Th2 cytokines during mucociliary differentiation contributes to antimicrobial defence by increasing the expression and release of selected antimicrobial peptides and mucus.     

Trophic niche partitioning of cryptic species of long-eared bats in Switzerland: implications for conservation

Dietary niche partitioning is postulated to play a major role for the stable coexistence of species within a community, particularly among cryptic species. Molecular markers have recently revealed the existence of a new cryptic species of long-eared bat, Plecotus macrobullaris, in the European Alps. We studied trophic niches as well as seasonal and regional variations of diet in eight colonies of the three Plecotus species occurring in Switzerland. Faeces were collected monthly from individuals returning to roost after foraging. Twenty-one arthropod categories were recognized from the faeces. All three species fed predominantly on Lepidoptera, which made up 41%, 87% and 88% (means across colonies) of the diet composition of P. auritus, P. macrobullaris and P. austriacus, respectively. The occurrence of numerous fragments of both diurnal and flightless insects in the diet of P. auritus (but rarely in the diet of the other two species) indicates that this species mostly gleans prey from substrates. P. austriacus and P. macrobullaris are more typical aerial feeders. The latter two species have narrow trophic niches, whilst P. auritus has a much broader diet. Comparison of intraspecific and interspecific niche overlaps in P. auritus and P. macrobullaris in sympatry suggests dietary niche partitioning between these two species. In contrast, the high similarity of the trophic niches of P. austriacus and P. macrobullaris, associated with a typical parapatric distribution, indicates competitive exclusion. The best conservation measures are preservation and restoration of habitats offering a high abundance of moths, the major prey of the three Plecotus species.     

DNA-methylation profiling distinguishes malignant melanomas from benign nevi

DNA methylation, an epigenetic alteration typically occurring early in cancer development, could aid in the molecular diagnosis of melanoma. We determined technical feasibility for high-throughput DNA-methylation array-based profiling using formalin-fixed paraffin-embedded tissues for selection of candidate DNA-methylation differences between melanomas and nevi. Promoter methylation was evaluated in 27 common benign nevi and 22 primary invasive melanomas using a 1505 CpG site microarray. Unsupervised hierarchical clustering distinguished melanomas from nevi; 26 CpG sites in 22 genes were identified with significantly different methylation levels between melanomas and nevi after adjustment for age, sex, and multiple comparisons and with β-value differences of ≥ 0.2. Prediction analysis for microarrays identified 12 CpG loci that were highly predictive of melanoma, with area under the receiver operating characteristic curves of > 0.95. Of our panel of 22 genes, 14 were statistically significant in an independent sample set of 29 nevi (including dysplastic nevi) and 25 primary invasive melanomas after adjustment for age, sex, and multiple comparisons. This first report of a DNA-methylation signature discriminating melanomas from nevi indicates that DNA methylation appears promising as an additional tool for enhancing melanoma diagnosis.