Comparative genomics of isolates of a pseudomonas aeruginosa epidemic strain associated with chronic lung infections of cystic fibrosis patients

Pseudomonas aeruginosa is the main cause of fatal chronic lung infections among individuals suffering from cystic fibrosis (CF). During the past 15 years, particularly aggressive strains transmitted among CF patients have been identified, initially in Europe and more recently in Canada. The aim of this study was to generate high-quality genome sequences for 7 isolates of the Liverpool epidemic strain (LES) from the United Kingdom and Canada representing different virulence characteristics in order to: (1) associate comparative genomics results with virulence factor variability and (2) identify genomic and/or phenotypic divergence between the two geographical locations. We performed phenotypic characterization of pyoverdine, pyocyanin, motility, biofilm formation, and proteolytic activity. We also assessed the degree of virulence using the Dictyostelium discoideum amoeba model. Comparative genomics analysis revealed at least one large deletion (40-50 kb) in 6 out of the 7 isolates compared to the reference genome of LESB58. These deletions correspond to prophages, which are known to increase the competitiveness of LESB58 in chronic lung infection. We also identified 308 non-synonymous polymorphisms, of which 28 were associated with virulence determinants and 52 with regulatory proteins. At the phenotypic level, isolates showed extensive variability in production of pyocyanin, pyoverdine, proteases and biofilm as well as in swimming motility, while being predominantly avirulent in the amoeba model. Isolates from the two continents were phylogenetically and phenotypically undistinguishable. Most regulatory mutations were isolate-specific and 29% of them were predicted to have high functional impact. Therefore, polymorphism in regulatory genes is likely to be an important basis for phenotypic diversity among LES isolates, which in turn might contribute to this strain's adaptability to varying conditions in the CF lung

Impact of Indian Total Sanitation Campaign on latrine coverage and use: a cross-sectional study in Orissa three years following programme implementation.

BACKGROUND: Faced with a massive shortfall in meeting sanitation targets, some governments have implemented campaigns that use subsidies focused on latrine construction to overcome income constraints and rapidly expand coverage. In settings like rural India where open defecation is common, this may result in sub-optimal compliance (use), thereby continuing to leave the population exposed to human excreta. METHODS: We conducted a cross-sectional study to investigate latrine coverage and use among 20 villages (447 households, 1933 individuals) in Orissa, India where the Government of India's Total Sanitation Campaign had been implemented at least three years previously. We defined coverage as the proportion of households that had a latrine; for use we identified the proportion of households with at least one reported user and among those, the extent of reported use by each member of the household. RESULTS: Mean latrine coverage among the villages was 72% (compared to <10% in comparable villages in the same district where the Total Sanitation Campaign had not yet been implemented), though three of the villages had less than 50% coverage. Among these households with latrines, more than a third (39%) were not being used by any member of the household. Well over a third (37%) of the members of households with latrines reported never defecating in their latrines. Less than half (47%) of the members of such households reported using their latrines at all times for defecation. Combined with the 28% of households that did not have latrines, it appears that most defecation events in these communities are still practiced in the open. CONCLUSION: A large-scale campaign to implement sanitation has achieved substantial gains in latrine coverage in this population. Nevertheless, gaps in coverage and widespread continuation of open defecation will result in continued exposure to human excreta, reducing the potential for health gains

Male-Produced Aggregation Pheromones of the Cerambycid Beetles Xylotrechus colonus and Sarosesthes fulminans

Adults of both sexes of the cerambycid beetles Xylotrechus colonus (F.) and Sarosesthes fulminans (F.) were attracted to odors produced by male conspecifics in olfactometer bioassays. Analyses of headspace volatiles from adults revealed that male X. colonus produced a blend of (R)- and (S)-3-hydroxyhexan-2-one and (2 S,3 S)- and (2R,3R)-2,3-hexanediol, whereas male S. fulminans produced (R)-3-hydroxyhexan-2-one and (2 S,3R)-2,3-hexanediol. All of these compounds were absent in the headspace of females. Two field bioassays were conducted to confirm the biological activity of the synthesized pheromones: (1) enantiomerically enriched pheromone components were tested singly and in species-specific blends and (2) four-component mixture of racemic 3-hydroxyhexan-2-one plus racemic 2-hydroxyhexan-3-one and the four-component blend of the stereoisomers of 2,3-hexanediols were tested separately and as a combined eight-component blend. In these experiments, adult male and female X. colonus were captured in greatest numbers in traps baited with the reconstructed blend of components produced by males, although significant numbers were also captured in traps baited with (R)-3-hydroxyhexan-2-one alone or in blends with other compounds. Too few adult S. fulminans were captured for a statistical comparison among treatments, but all were caught in traps baited with lures containing (R)-3-hydroxyhexan-2-one. In addition to these two species, adults of two other species of cerambycid beetles, for which pheromones had previously been identified, were caught: Neoclytus a. acuminatus (F.) and its congener Neoclytus m. mucronatus (F.). Cross-attraction of beetles to pheromone blends of other species, and to individual pheromone components that are shared by two or more sympatric species, may facilitate location of larval hosts by species that compete for the same host species

Phylogeny, Diet, and Cranial Integration in Australodelphian Marsupials

Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials

Population genomics of sub-Saharan Drosophila melanogaster: African diversity and non-African admixture

(ABRIDGED) We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were sequenced above 25X depth from haploid embryos. Results indicated a pervasive influence of non-African admixture in many African populations, motivating the development and application of a novel admixture detection method. Admixture proportions varied among populations, with greater admixture in urban locations. Admixture levels also varied across the genome, with localized peaks and valleys suggestive of a non-neutral introgression process. Genomes from the same location differed starkly in ancestry, suggesting that isolation mechanisms may exist within African populations. After removing putatively admixed genomic segments, the greatest genetic diversity was observed in southern Africa (e.g. Zambia), while diversity in other populations was largely consistent with a geographic expansion from this potentially ancestral region. The European population showed different levels of diversity reduction on each chromosome arm, and some African populations displayed chromosome arm-specific diversity reductions. Inversions in the European sample were associated with strong elevations in diversity across chromosome arms. Genomic scans were conducted to identify loci that may represent targets of positive selection. A disproportionate number of candidate selective sweep regions were located near genes with varied roles in gene regulation. Outliers for Europe-Africa FST were found to be enriched in genomic regions of locally elevated cosmopolitan admixture, possibly reflecting a role for some of these loci in driving the introgression of non-African alleles into African populations

Protein Expression Redirects Vesicular Stomatitis Virus RNA Synthesis to Cytoplasmic Inclusions

Positive-strand and double-strand RNA viruses typically compartmentalize their replication machinery in infected cells. This is thought to shield viral RNA from detection by innate immune sensors and favor RNA synthesis. The picture for the non-segmented negative-strand (NNS) RNA viruses, however, is less clear. Working with vesicular stomatitis virus (VSV), a prototype of the NNS RNA viruses, we examined the location of the viral replication machinery and RNA synthesis in cells. By short-term labeling of viral RNA with 5′-bromouridine 5′-triphosphate (BrUTP), we demonstrate that primary mRNA synthesis occurs throughout the host cell cytoplasm. Protein synthesis results in the formation of inclusions that contain the viral RNA synthesis machinery and become the predominant sites of mRNA synthesis in the cell. Disruption of the microtubule network by treatment of cells with nocodazole leads to the accumulation of viral mRNA in discrete structures that decorate the surface of the inclusions. By pulse-chase analysis of the mRNA, we find that viral transcripts synthesized at the inclusions are transported away from the inclusions in a microtubule-dependent manner. Metabolic labeling of viral proteins revealed that inhibiting this transport step diminished the rate of translation. Collectively those data suggest that microtubule-dependent transport of viral mRNAs from inclusions facilitates their translation. Our experiments also show that during a VSV infection, protein synthesis is required to redirect viral RNA synthesis to intracytoplasmic inclusions. As viral RNA synthesis is initially unrestricted, we speculate that its subsequent confinement to inclusions might reflect a cellular response to infection

The effect of low temperature and low light intensity on nutrient removal from municipal wastewater by purple phototrophic bacteria (PPB)

There has been increased interest in alternative wastewater treatment systems to improve nutrient recovery while achieving acceptable TCOD, TN, and TP discharge limits. Purple phototrophic bacteria (PPB) have a high potential for simultaneous nutrient removal and recovery from wastewater. This study evaluated the PPB performance and its growth at different operating conditions with a focus on HRT and light optimization using a continuous-flow membrane photobioreactor (PHB). Furthermore, the effect of low temperature on PPB performance was assessed to evaluate the PPB’s application in cold-climate regions. In order to evaluate PPB performance, TCOD, TN, and TP removal efficiencies and Monod kinetic parameters were analyzed at different HRTs (36, 18, and 9 h), at temperatures of 22°C and 11°C and infrared (IR) light intensities of 50, 3, and 1.4 Wm-2. The results indicated that low temperature had no detrimental impact on PPB’s performance. The photobioreactor (PHB) with cold-enriched PPB has a high potential to treat municipal wastewater with effluent concentrations below target limits (TCOD˂ 50mgL-1, TN˂10 mgL-1, and TP˂1 mgL-1). Monod kinetic parameters Ks, K, Y, and Kd were estimated at 20-29 mgCODL-1, 1.6-1.9 mgCOD(mgVSS.d)-1, 0.47 mgVSS mgCOD-1, and 0.07-0.08 d-1 at temperatures of 11°C-22°C respectively. The results of the steady-state mass balances showed TCOD, TN, and TP recoveries of 80%-86%, which reflected PPB’s substrate and nutrient assimilation. Previous studies utilized high light intensities (˃ 50 Wm-2) to provide PPB with the maximum energy required for its growth. In order to enable the PPB technology as a practical approach in municipal wastewater treatment, light intensity must be optimized. Based on the literature, there is no study on PPB performance at low light intensities using a continuous-flow membrane photobioreactor. The effect of low light intensities of 3, and 1.4 Wm-2 on PPB performance was addressed in this study. The results indicated that PPB at a light intensity as low as 1.4 Wm-2 were able to treat municipal wastewater with effluent concentrations below above-mentioned target limits. Light intensity (1-50 Wm-2) had no detrimental impact on PPB performance and Monod kinetic parameters. This study showed that the optimized light intensity required for municipal wastewater treatment with PPB is significantly lower than previously indicated in the literature. The energy consumptions attributed to PHB’s illumination of 3, and 1.4 Wm-2 were determined to be 1.44, and 0.67 kWh/m3 which is significantly lower than previous studies (˃ 24 kWh/m3)

hSAGEing: An Improved SAGE-Based Software for Identification of Human Tissue-Specific or Common Tumor Markers and Suppressors

SAGE (serial analysis of gene expression) is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers.To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique “multi-pool method” that analyzes multiple pools of pair-wise case controls individually. When all the settings are in “inclusion”, the common SAGE tag sequences are mined. When one tissue type is in “inclusion” and the other types of tissues are not in “inclusion”, the selected tissue-specific SAGE tag sequences are generated. They are displayed in tags-per-million (TPM) and fold values, as well as visually displayed in four kinds of scales in a color gradient pattern. In the fold visualization display, the top scores of the SAGE tag sequences are provided, along with cluster plots. A user-defined matrix file is designed for cross-tissue comparison by selecting libraries from publically available databases or user-defined libraries

Minimum information about an uncultivated virus genome (MIUVIG)

This is the final version. Available on open access from Nature Research via the DOI in this recordNOTE: the full list of funders and grants is in the acknowledgements section of the articleWe present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.Simons Foundation InternationalNatural Environment Research Council (NERC