Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton

Cyanorak v2.1 : a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms

Predictive factors of difficult implantation procedure in cardiac resynchronisation therapy

Les guidelines actuelles recommandent l'implantation d'un stimulateur ou d'un défibrillateur resynchronisateur (CRT) chez le patient insuffisant cardiaque, symptomatique en stade III-IV de la NYHA, avec dysfonction systolique majeure et critère d'asynchronisme électrique, malgré un traitement médical optimal. De nombreux essais cliniques ont montré un bénéfice clinique important du CRT avec une réduction de la morbimortalité. Problématique. La procédure est parfois longue et difficile avec un taux de complications proche de 10% et un taux d'échec d'implantation primaire de 5 à 10% selon les études. Il n'existe peu de travaux à notre connaissance sur l'évaluation des facteurs prédictifs de difficulté ou d'échec lors de la primo-implantation de la sonde VG alors même qu'il a été démontré une corrélation significative entre le temps de procédure lors de l'implantation d'un CRT et certains paramètres comme les reprises chirurgicales, le taux de complications et le taux d'infection. Les Objectifs de notre étude étaient : (1) d'évaluer la prévalence et les facteurs prédictifs des procédures difficiles définies comme longues (>=88 minutes) ; (2) d'évaluer les facteurs prédictifs de l'échec de la mise en place de la sonde VG lors de la primo-implantation. Méthodologie. Il s'agit d'une étude prospective de 128 patients hospitalisés entre novembre 2008 et septembre 2009 dans notre service pour mise en place d'un CRT. Résultats. Le taux de prévalence de procédures difficiles est de 23%. En analyse univariée, les facteurs prédictifs d'une implantation difficile sont la fraction d'éjection basse et la dilatation des cavités cardiaques gauches. En analyse multivariée, les facteurs indépendants sont l'échec de l'implantation de la sonde VG lors de la première implantation et la dilatation des cavités cardiaques. La dilatation des cavités cardiaques est également le seul facteur indépendant prédictif de l'échec de la mise en place de la sonde VG lors de la primo-implantation.Conclusion. La sévérité de la dysfonction VG et la dilatation des cavités cardiaques apparaissent comme les seuls facteurs prédictifs de difficulté et d'échec de la mise en place de la sonde VG via le sinus coronaire, incitant donc à une sélection précoce des patients insuffisants cardiaques.ST ETIENNE-BU Médecine (422182102) / SudocSudocFranceF

A single-centre experience concerning the safety of Sprint Fidelis defibrillator lead extraction at the time of pulse generator replacement or in case of evidence of lead failure

SummaryBackgroundThe reported failure rate of the Sprint Fidelis defibrillator lead (SFDL) has increased more than initially expected, with emerging evidence of accelerating fracture rates. Current consensus guidelines continue to discourage prophylactic lead extraction, citing major complication rates of 1.4–7.3%. Therefore, data relating to the risks of systematic SFDL extraction are lacking, with no methodical extraction protocol reported to date. Moreover, few statistical analyses have identified predictors of SFDL failure.ObjectivesThe aims of this single-centre study were: to examine the safety and feasibility of systematic SFDL extraction at the time of pulse generator replacement or in case of lead failure; and to identify predictors of SFDL failure.MethodsBetween January 2005 and October 2007, 218 consecutive patients underwent transvenous SFDL implantation in our centre.ResultsDuring a mean follow-up of 43±15months, SFDL extraction was performed in 49 patients (22.5%) for the following reasons: inappropriate shocks (n=21; 9.6%), systematic extraction at time of pulse generator extraction (n=23; 10.5%), high impedance (n=3; 1.4%), high SFDL threshold (n=1; 0.4%) and cardiac device-related infection (n=1; 0.4%). No severe complications occurred, although two minor complications were reported (lead dislodgments). SFDL fracture was observed in 25 patients (11.5%; 3.2%/year incidence). The only predictor associated with SFDL fracture was the number of leads (P=0.01).ConclusionIn our series, SFDL extraction at the time of pulse generator extraction or in case of evidence of lead failure was feasible and safe. Number of leads was identified as a new predictive factor for SFDL fracture