Network analysis of plasmidomes: the Azospirillum brasilense Sp245 case

Azospirillum brasilense is a nitrogen-fixing bacterium living in association with plant roots. The genome of the strain Sp245, isolated in Brazil from wheat roots, consists of one chromosome and six plasmids. In this work, the A. brasilense Sp245 plasmids were analyzed in order to shed some light on the evolutionary pathways they followed over time. To this purpose, a similarity network approach was applied in order to identify the evolutionary relationships among all the A. brasilense plasmids encoded proteins; in this context a computational pipeline specifically devoted to the analysis and the visualization of the network-like evolutionary relationships among different plasmids molecules was developed. This information was supplemented with a detailed (in silico) functional characterization of both the connected (i.e., sharing homology with other sequences in the dataset) and the unconnected (i.e., not sharing homology) components of the network. Furthermore, the most likely source organism for each of the genes encoded by A. brasilense plasmids was checked, allowing the identification of possible trends of gene loss/gain in this microorganism. Data obtained provided a detailed description of the evolutionary landscape of the plasmids of A. brasilense Sp245, suggesting some of the molecular mechanisms responsible for the present-day structure of these molecules

Symptomatic remission and patient quality of life in an observational study of schizophrenia: Is there a relationship?

This analysis aimed to examine the association between remission and quality of life (QOL) in schizophrenia. In post-hoc analyses of the 3-year, prospective, observational Schizophrenia Outpatients Health Outcomes (SOHO) study, we compared the QOL of patients who achieved symptomatic and clinical remission with those who did not, and the factors associated. Symptomatic remission was defined as achieving a score of ≤3 on the Clinical Global Impression-Schizophrenia (CGI-SCH) scale, maintained for 6 months and without hospitalization. QOL was patient self-rated using the European-QOL. Of the 6516 patients analyzed, 38% were in symptomatic remission 12 months post-baseline and 52% at 36 months. Functional remission remained fairly constant from 12 months to 36 months (22.4% at both time points). At all visits from 12 to 36 months, patient QOL and social functioning were significantly higher for patients in symptomatic remission. QOL was higher in patients in functional remission. Patients with maintained symptomatic remission over the 3-year follow-up had a much greater improvement in QOL than patients with no symptomatic remission or symptomatic remission for part of the period. Factors associated with a better QOL also included paid employment, socially active, a higher CGI-SCH cognitive score, good compliance, and a better baseline QOL

Origin, duplication and reshuffling of plasmid genes: Insights from Burkholderia vietnamiensis G4 genome.

Using a computational pipeline based on similarity networks reconstruction we analysed the 1133 genes of the Burkholderia vietnamiensis ( Bv) G4 five plasmids, showing that gene and operon duplication played an important role in shaping the plasmid architecture. Several single/multiple duplications occurring at intra- and/or interplasmids level involving 253 paralogous genes (stand-alone, clustered or operons) were detected. An extensive gene/operon exchange between plasmids and chromosomes was also disclosed. The larger the plasmid, the higher the number and size of paralogous fragments. Many paralogs encoded mobile genetic elements and duplicated very recently, suggesting that the rearrangement of the Bv plastic genome is ongoing. Concerning the "molecular habitat" and the "taxonomical status" (the Preferential Organismal Sharing) of Bv plasmid genes, most of them have been exchanged with other plasmids of bacteria belonging (or phylogenetically very close) to Burkholderia, suggesting that taxonomical proximity of bacterial strains is a crucial issue in plasmid-mediated gene exchange. © 2014 Elsevier Inc

Archival Legacy Investigations of Circumstellar Environments: Overview and First Results

We are currently conducting a comprehensive and consistent re-processing of archival HST-NICMOS coronagraphic surveys using advanced PSF subtraction methods, entitled the Archival Legacy Investigations of Circumstellar Environments program (ALICE, HST/AR 12652). This virtual campaign of about 400 targets has already produced numerous new detections of previously unidentified point sources and circumstellar structures. We present five newly spatially resolved debris disks revealed in scattered light by our analysis of the archival data. These images provide new views of material around young solar-type stars at ages corresponding to the period of terrestrial planet formation in our solar system. We have also detected several new candidate substellar companions, for which there are ongoing followup campaigns (HST/WFC3 and VLT/SINFONI in ADI mode). Since the methods developed as part of ALICE are directly applicable to future missions (JWST, AFTA coronagraph) we emphasize the importance of devising optimal PSF subtraction methods for upcoming coronagraphic imaging missions. We describe efforts in defining direct imaging high-level science products (HLSP) standards that can be applicable to other coronagraphic campaigns, including ground-based (e.g., Gemini Planet Imager), and future space instruments (e.g., JWST). ALICE will deliver a first release of HLSPs to the community through the MAST archive at STScI in 2014.Comment: Proceedings of the SPIE, 9143-199. 17 pages, 11 figure

Exploring the HME and HAE1 efflux systems in the genus Burkholderia

<p>Abstract</p> <p>Background</p> <p>The genus <it>Burkholderia </it>includes a variety of species with opportunistic human pathogenic strains, whose increasing global resistance to antibiotics has become a public health problem. In this context a major role could be played by multidrug efflux pumps belonging to Resistance Nodulation Cell-Division (RND) family, which allow bacterial cells to extrude a wide range of different substrates, including antibiotics. This study aims to i) identify <it>rnd </it>genes in the 21 available completely sequenced <it>Burkholderia </it>genomes, ii) analyze their phylogenetic distribution, iii) define the putative function(s) that RND proteins perform within the <it>Burkholderia </it>genus and iv) try tracing the evolutionary history of some of these genes in <it>Burkholderia</it>.</p> <p>Results</p> <p>BLAST analysis of the 21 <it>Burkholderia </it>sequenced genomes, using experimentally characterized <it>ceoB </it>sequence (one of the RND family counterpart in the genus <it>Burkholderia</it>) as probe, allowed the assembly of a dataset comprising 254 putative RND proteins. An extensive phylogenetic analysis revealed the occurrence of several independent events of gene loss and duplication across the different lineages of the genus <it>Burkholderia</it>, leading to notable differences in the number of paralogs between different genomes. A putative substrate [antibiotics (HAE1 proteins)/heavy-metal (HME proteins)] was also assigned to the majority of these proteins. No correlation was found between the ecological niche and the lifestyle of <it>Burkholderia </it>strains and the number/type of efflux pumps they possessed, while a relation can be found with genome size and taxonomy. Remarkably, we observed that only HAE1 proteins are mainly responsible for the different number of proteins observed in strains of the same species. Data concerning both the distribution and the phylogenetic analysis of the HAE1 and HME in the <it>Burkholderia </it>genus allowed depicting a likely evolutionary model accounting for the evolution and spreading of HME and HAE1 systems in the <it>Burkholderia </it>genus.</p> <p>Conclusion</p> <p>A complete knowledge of the presence and distribution of RND proteins in <it>Burkholderia </it>species was obtained and an evolutionary model was depicted. Data presented in this work may serve as a basis for future experimental tests, focused especially on HAE1 proteins, aimed at the identification of novel targets in antimicrobial therapy against <it>Burkholderia </it>species.</p

Influence of the Radio-Frequency source properties on RF-based atom traps

We discuss the quality required for the RF source used to trap neutral atoms in RF-dressed potentials. We illustrate this discussion with experimental results obtained on a Bose-Einstein condensation experiment with different RF sources.Comment: 5 figures, 7 page