HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.Animal science

Mining Virulence Genes Using Metagenomics

When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens

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

Selection in Coastal Synechococcus (Cyanobacteria) Populations Evaluated from Environmental Metagenomes

Environmental metagenomics provides snippets of genomic sequences from all organisms in an environmental sample and are an unprecedented resource of information for investigating microbial population genetics. Current analytical methods, however, are poorly equipped to handle metagenomic data, particularly of short, unlinked sequences. A custom analytical pipeline was developed to calculate dN/dS ratios, a common metric to evaluate the role of selection in the evolution of a gene, from environmental metagenomes sequenced using 454 technology of flow-sorted populations of marine Synechococcus, the dominant cyanobacteria in coastal environments. The large majority of genes (98%) have evolved under purifying selection (dN/dS<1). The metagenome sequence coverage of the reference genomes was not uniform and genes that were highly represented in the environment (i.e. high read coverage) tended to be more evolutionarily conserved. Of the genes that may have evolved under positive selection (dN/dS>1), 77 out of 83 (93%) were hypothetical. Notable among annotated genes, ribosomal protein L35 appears to be under positive selection in one Synechococcus population. Other annotated genes, in particular a possible porin, a large-conductance mechanosensitive channel, an ATP binding component of an ABC transporter, and a homologue of a pilus retraction protein had regions of the gene with elevated dN/dS. With the increasing use of next-generation sequencing in metagenomic investigations of microbial diversity and ecology, analytical methods need to accommodate the peculiarities of these data streams. By developing a means to analyze population diversity data from these environmental metagenomes, we have provided the first insight into the role of selection in the evolution of Synechococcus, a globally significant primary producer

Neotectonics of the SW Iberia margin, Gulf of Cadiz and Alboran Sea: a reassessment including recent structural, seismic and geodetic data

We use a thin-shell approximation for the lithosphere to model the neotectonics of the Gulf of Cadiz, SW Iberia margin and the westernmost Mediterranean, in the eastern segment of the Azores-Gibraltar plate boundary. In relation to previous neotectonic models in the region, we utilize a better constrained structural map offshore, and the recent GPS measurements over NW Africa and Iberia have been taken into account, together with the seismic strain rate and stress data, to evaluate alternative geodynamic settings proposed for the region. We show that by assuming a relatively simple, two-plate tectonic framework, where Nubia and Eurasia converge NW-SE to WNW-ESE at a rate of 4.5-6 mm yr-1, the models correctly predict the amount of shortening and wrenching between northern Algeria-Morocco and southern Spain and between NW Morocco and SW Iberia, as estimated from both GPS data and geological constraints. The consistency between modelled and observed velocities in the vicinity of Gibraltar and NW Morocco indicates that forcing by slab sinking beneath Gibraltar is not required to reproduce current horizontal deformation in these areas. In the Gulf of Cadiz and SW Iberia, the modelling results support a diffuse Nubia-Eurasia Plate boundary, where the convergence is accommodated along NNE-SSW to NE-SW and ENE-WSW thrust faults and WNW-ESE right-lateral strike-slip faults, over an area >200 km wide, in good general agreement with the distribution of the seismic strain rate and associated faulting mechanisms. The modelling results are robust to regional uncertainties in the structure of the lithosphere and have important implications for the earthquake and tsunami hazard of Portugal, SW Spain and Morocco. We predict maximum, long-term average fault slip rates between 1-2 mm yr-1, that is, less than 50 per cent the average plate relative movement, suggesting very long return periods for high-magnitude (Mw > 8) earthquakes on individual structures.publishe

Going Deeper: Metagenome of a Hadopelagic Microbial Community

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above

Association of Candidate Gene Polymorphisms With Chronic Kidney Disease: Results of a Case-Control Analysis in the Nefrona Cohort

Chronic kidney disease (CKD) is a major risk factor for end-stage renal disease, cardiovascular disease and premature death. Despite classical clinical risk factors for CKD and some genetic risk factors have been identified, the residual risk observed in prediction models is still high. Therefore, new risk factors need to be identified in order to better predict the risk of CKD in the population. Here, we analyzed the genetic association of 79 SNPs of proteins associated with mineral metabolism disturbances with CKD in a cohort that includes 2, 445 CKD cases and 559 controls. Genotyping was performed with matrix assisted laser desorption ionizationtime of flight mass spectrometry. We used logistic regression models considering different genetic inheritance models to assess the association of the SNPs with the prevalence of CKD, adjusting for known risk factors. Eight SNPs (rs1126616, rs35068180, rs2238135, rs1800247, rs385564, rs4236, rs2248359, and rs1564858) were associated with CKD even after adjusting by sex, age and race. A model containing five of these SNPs (rs1126616, rs35068180, rs1800247, rs4236, and rs2248359), diabetes and hypertension showed better performance than models considering only clinical risk factors, significantly increasing the area under the curve of the model without polymorphisms. Furthermore, one of the SNPs (the rs2248359) showed an interaction with hypertension, being the risk genotype affecting only hypertensive patients. We conclude that 5 SNPs related to proteins implicated in mineral metabolism disturbances (Osteopontin, osteocalcin, matrix gla protein, matrix metalloprotease 3 and 24 hydroxylase) are associated to an increased risk of suffering CKD

How do Mediterranean shrub species cope with shade? Ecophysiological response to different light intensities

Under natural conditions, light exposure for Mediterranean shrubs can be highly variable, especially during cloudy days or under a canopy, and can interfere with other environmental factors such as temperature and water availability. With the aim of decoupling the effect of radiation and temperature from water availability, we conducted an experiment where two perennial and three summer semi-deciduous shrub species were subjected to different levels of irradiation. In order to follow plant responses to light exposure, we measured gas exchange, photosystem II photochemical efficiency, photosynthetic pigments and leaf mass area in spring and summer. Results showed that all study species presented a plastic response to different light conditions, and that light-related traits varied in a coordinated manner. Summer semi-deciduous species exhibited a more opportunistic response, with higher photosynthesis rates in full sun, but under shade conditions, the two strategies presented similar assimilation rates. Stomatal conductance did not show such a drastic response as photosynthetsis, being related to changes in WUE. Daily cycles of F/F revealed a slight photoinhibitory response during summer, mainly in perennial species. In all cases photosynthetic pigments adjusted to the radiation level; leaves had lower chlorophyll content, higher pool of xanthophylls and higher proportion of the de-epoxydaded state of xanthophylls under sun conditions. Lutein content increased in relation to the xanthophyll pool under shade conditions. Our results evidenced that radiation is an important driving factor controlling morphological and physiological status of Mediterranean shrub species, independently of water availability. Summer semi-deciduous species exhibit a set of traits with higher response variability, maximising their photosynthetic assimilation under different sun conditions

Probing the adsorption/desorption of amphiphilic polymers at the air-water interface during large interfacial deformations

Hydrophobically modified polymers are good candidates for the stabilization of liquid interfaces thanks to the high anchoring energy of the hydrophobic parts. In this article we probe the interfacial anchoring of a series of home-made hydrophobically modified polymers of controlled degree of grafting by studying their behavior upon large area dilations and compressions. By comparing the measured interfacial tension to the one that we expect in the case of a constant number of adsorbed monomers, we are able to deduce whether desorption or adsorption occurs during area variations. We find that the polymer chains with the longest hydrophobic grafts desorb for larger compressions than the polymers with the shortest grafts, because of their larger desorption energy. Furthermore, we observe more desorption for polymers with the highest grafting densities. We attribute this counter intuitive result to the fact that for high grafting densities, the length of the polymer loops is shorter, hence the elastic penalty upon compression is larger for these layers, leading to a faster desorption. The dilatation experiments reveal that the number of adsorbed anchors remains constant in the case of chains with low grafting density while chains with the highest degree of grafting seem to show some degree of adsorption during the dilatation. Therefore for these highly grafted chains there may be unadsorbed grafts remaining in the vicinity of the interface, which may adsorb quickly to the interface upon dilatation.Interfaces liquides recouvertes de multi-couches de polymèresMousses de lixiviation pour l'extraction de métaux des déchets électronique