An ecosystem-based approach to assess the status of Mediterranean algae-dominated shallow rocky reefs.

A conceptual model was constructed for the functioning the algae-dominated rocky reef ecosystem of the Mediterranean Sea. The Ecosystem-Based Quality Index (reef-EBQI) is based upon this model. This index meets the objectives of the EU Marine Strategy Framework Directive. It is based upon (i) the weighting of each compartment, according to its importance in the functioning of the ecosystem; (ii) biological parameters assessing the state of each compartment; (iii) the aggregation of these parameters, assessing the quality of the ecosystem functioning, for each site; (iv) and a Confidence Index measuring the reliability of the index, for each site. The reef-EBQI was used at 40 sites in the northwestern Mediterranean. It constitutes an efficient tool, because it is based upon a wide set of functional compartments, rather than upon just a few species; it is easy and inexpensive to implement, robust and not redundant with regard to already existing indices

PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection

By engulfing potentially harmful microbes, professional phagocytes are continually at risk from intracellular pathogens. To avoid becoming infected, the host must kill pathogens in the phagosome before they can escape or establish a survival niche. Here, we analyse the role of the phosphoinositide (PI) 5-kinase PIKfyve in phagosome maturation and killing, using the amoeba and model phagocyte Dictyostelium discoideum. PIKfyve plays important but poorly understood roles in vesicular trafficking by catalysing formation of the lipids phosphatidylinositol (3,5)-bisphosphate (PI(3,5)2) and phosphatidylinositol-5-phosphate (PI(5)P). Here we show that its activity is essential during early phagosome maturation in Dictyostelium. Disruption of PIKfyve inhibited delivery of both the vacuolar V-ATPase and proteases, dramatically reducing the ability of cells to acidify newly formed phagosomes and digest their contents. Consequently, PIKfyve- cells were unable to generate an effective antimicrobial environment and efficiently kill captured bacteria. Moreover, we demonstrate that cells lacking PIKfyve are more susceptible to infection by the intracellular pathogen Legionella pneumophila. We conclude that PIKfyve-catalysed phosphoinositide production plays a crucial and general role in ensuring early phagosomal maturation, protecting host cells from diverse pathogenic microbes

Assessing the Diversity and Specificity of Two Freshwater Viral Communities through Metagenomics

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale

Blue and Red Light Modulates SigB-Dependent Gene Transcription, Swimming Motility and Invasiveness in Listeria monocytogenes

Background: In a number of gram-positive bacteria, including Listeria, the general stress response is regulated by the alternative sigma factor B (SigB). Common stressors which lead to the activation of SigB and the SigB-dependent regulon are high osmolarity, acid and several more. Recently is has been shown that also blue and red light activates SigB in Bacillus subtilis. Methodology/Principal Findings: By qRT-PCR we analyzed the transcriptional response of the pathogen L. monocytogenes to blue and red light in wild type bacteria and in isogenic deletion mutants for the putative blue-light receptor Lmo0799 and the stress sigma factor SigB. It was found that both blue (455 nm) and red (625 nm) light induced the transcription of sigB and SigB-dependent genes, this induction was completely abolished in the SigB mutant. The blue-light effect was largely dependent on Lmo0799, proving that this protein is a genuine blue-light receptor. The deletion of lmo0799 enhanced the red-light effect, the underlying mechanism as well as that of SigB activation by red light remains unknown. Blue light led to an increased transcription of the internalin A/B genes and of bacterial invasiveness for Caco-2 enterocytes. Exposure to blue light also strongly inhibited swimming motility of the bacteria in a Lmo0799- and SigB-dependent manner, red light had no effect there. Conclusions/Significance: Our data established that visible, in particular blue light is an important environmental signal with an impact on gene expression and physiology of the non-phototrophic bacterium L. monocytogenes. In natural environments these effects will result in sometimes random but potentially also cyclic fluctuations of gene activity, depending on the light conditions prevailing in the respective habitat

Low temperature diffusion of impurities in hydrogen implanted silicon

4 p.International audienceThe effect of hydrogen implantation on the transport of impurities in silicon is studied. We use secondary ion mass spectrometry measurements to investigate the depth redistribution of oxygen, carbon, and fluorine during low temperature, ≤ 450 °C, isothermal anneals. Their fast migration toward the projected range region of H implants points to the existence of a strong interaction of the impurities with H-induced defects. Significantly enhanced, as compared to the literature values, diffusivities of the investigated impurities were obtained. The results reveal that hydrogen implantation can be advantageously used for the impurity profile engineering and gettering studies in silicon in the low temperatures annealing regime

Impact of the transient formation of molecular hydrogen on the microcrack nucleation and evolution in H-implanted Si (001)

International audienceWe study the implant-induced hydrogenated defects responsible for the Smart Cut™ layer transfer of Si 001 films. Different experimental methods are used to quantify the time dependence of the defect evolution and interactions during isothermal annealings. An optical characterization technique was developed for the statistical analysis of the formation and growth of micrometer size microcracks in the buried implanted layer. We show that the formation of molecular hydrogen is dominated by a transient phenomenon related to the rapid dissociation of the hydrogenated point defects. The impact of the H 2 formation kinetics on the microcrack evolution is described and the physical mechanisms involved in their growth are identified. A comprehensive picture of the fracture phenomenon in H implanted Si leading to the full layer transfer is proposed and discussed

Time dependence study of hydrogen-induced defects in silicon during thermal anneals

International audienceHydrogen implantation in silicon and subsequent thermal anneal result in the formation of a wide range of point and extended defects. In particular, characteristic two-dimensional extended defects, i.e. platelets, are formed. The growth of these defects during thermal anneal, related to H migration, induces the development of micro-cracks in Si. In this paper, a time dependence study of H defects during isothermal anneals is performed using SIMS, FTIR and TEM techniques. We calculate the kinetics of H 2 formation based on SIMS depth profiling and FTIR measurements. We show that the splitting is determined by H migration and rearrangement of hydrogenated defects

Structuring factors and processes of microbial food webs in French large lakes

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