Phylogénie moléculaire et éléments de biogéographie de trois lignées importantes des communautés d eucaryotes unicellulaires en milieu marin (les Chloroplastida, les Radiolaria et les Alveolata)

Les picoeucaryotes (eucaryotes inférieurs à 3 microns) sont des acteurs clés des écosystèmes marins. Ce travail vise à mieux définir leur diversité génétique à l aide de bibliothèques génétique du gène de l ARN 18S. En Méditerranée, les algues vertes picoplanctoniques sont principalement des prasinophytes. Des organismes inconnus sont détectés à différents niveaux taxonomiques. Les assemblages de prasinophytes varient selon le niveau trophique et le gradient lumineux vertical. Les Radiolaria sont des hétérotrophes microplanctoniques vivant en symbiose avec des eucaryotes photosynthétiques unicellulaires.. Treize nouveaux clades sont détectés dans le picoplancton. Les Radiolaria sont retrouvés uniquement en milieu marin où ils semblent préférer les eaux oligotrophes aphotiques. L ordre des Syndiniales regroupe des parasites. Quatre nouveaux clades dont trois sans représentant en culture sont définis. Les Syndiniales sont strictement marins et peuplent l ensemble des habitats.PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes

18 pages, 9 figures, 3 tables.-- Supporting information (Suppl. tables S1-S7, 20 pages) available at: https://doi.org/10.1016/j.dsr.2008.06.007Protists, and among them the picoeukaryotes (cells<3 μm), have been described as significant contributors to both carbon biomass and production in oligotrophic regions of the oceans. However, protist assemblages remain largely undescribed in pelagic ecosystems and in particular in the Indian Ocean. In the present work, we investigated protists along an eastward transect across the sub-tropical gyre of the Indian Ocean (from South Africa to Australia), with a particular focus on picoeukaryotes. We combined inverted and epifluorescence microscopy, flow cytometry, pigment analysis, denaturing gel gradient electrophoresis (DGGE), 18S rDNA clone libraries, and fluorescent in situ hybridization (FISH). Overall the picophytoplankton fraction contributed 88% and 90% of total Chl a at the surface and DCM, respectively, with picoeukaryotes accounting for 38% and 50% of total Chl a at the surface and DCM. Considering only the Indian South Subtropical Gyre (ISSG) province, we observed greater shifts in the picoeukaryotic assemblage throughout the upper 200 m of the water column than along the ca. 10,000 km cruise track. In terms of taxonomic diversity and contribution of each taxon to the picoeukaryotic community, prasinophytes were well represented at more coastal stations with the genus Micromonas reaching densities up to 750 cell mL−1 in coastal waters and less than 100 cell mL−1 at open ocean stations. Haptophytes (56% and 45% of picoeukaryotic pigments at surface and DCM, respectively) and possibly pelagophytes (28% and 40% of picoeukaryotic pigments at surface and DCM, respectively) appeared to be dominant at open ocean stations. Other groups and in particular organisms affiliated to chrysophytes, and to a lesser extent to cryptophytes, appear as clear targets for future qualitative and quantitative studies. Moreover, the occurrence of many sequences related to radiolarians (5% and 27% at surface and DCM, respectively) will require further investigationThis work was funded by projects TRANSINDICO (REN2002-10951-E/MAR, MCyT) to R.M. and PicOcean to D.V., and NSF Grant OCE02-21063 to E.G. and M.D. Ohman funded the ship time. F.N. was supported by a doctoral fellowship from the French Research MinistryPeer reviewe

An annotated checklist of Marine Phytoplankton taxa at the SOMLIT-Astan time series off Roscoff (Western English Channel, France): data collected from 2000 to 2010

International audienceA checklist of micro-phytoplankton. taxa based on net tow and Niskin bottle samples taken twice a month during the periods 2000-2003 and 2006-2010 at station SOMLIT-Astan (north of Roscoff, Western English Channel, France) is presented. SOMLIT-Astan is a coastal long-term monitoring station. It was established off Roscoff, where the water column seldom becomes stratified, and where continental influence is limited. Taxonomic identification was done based on light microscopy observations. The checklist includes 178 taxa (genus or species) among which 70 genera and 131 species of diatoms are recorded. Diatoms with benthic affinities make up 51% of the list of diatoms genera identified. Guinardia (especially G. delicatula) and Paralia sulcata appear as key taxa, becoming dominant in spring/summer and winter, respectively. Dinoflagellates are less diversified and never dominate. This work although not exhaustive, provides a reference list for micro-phytoplankton off Roscoff, and more generally for the permanently mixed waters of the Western English Channel, as well as information on the most common and/or abundant taxa in this habitat

Temporal trends in healthcare resource use and associated costs of patients with cystic fibrosis

Background: Better insights into the natural course of cystic fibrosis (CF) have led to treatment approaches that have improved pulmonary health and increased the life expectancy of affected individuals. This study evaluated how the combination of modified demographics and changes in CF management impacted resource consumption and the cost of care.Methods: Medical records of CF patients from 2006 to 2016 in the French CF Registry were linked to their corresponding claims data (SNDS). Medications, medical visits, procedures, hospitalisations, and indirect costs were annualized by calendar year from 2006 to 2017.Results: Of the 7,671 patients included in the French CF Registry, 6,187 patients (80.7%) were linked to the SNDS (51.9% male, mean age = 24.7 years). The average cost per patient was €14,174 in 2006, €21,920 in 2011 and €44,585 in 2017. Costs associated with hospital stays increased from €3,843 per patient in 2006 to €6,741 in 2017. In 2017, the mean cost per CF patient was allocated as follows: 72% for medications (of which 51% for modulator therapies), 15% for hospital stays, 7% for medical visits, 3% for indirect costs, 2% for medical devices, 1% for outpatient medical procedures.Conclusion: There was a strong increase in the mean annual cost per CF patient between 2006 and 2017, mostly due to the cost of therapy after the introduction of cystic fibrosis transmembrane conductance regulator (CFTR) modulators. The combination of an increase in the number of CF patients - particularly adult patients - and an increase in the annual cost per patient led to a substantial increase in the total cost of CF disease care for the health systems.Keywords: Costs; Cystic fibrosis; Healthcare resource use; Observational study

Table_1_Cancer incidence and prevalence in cystic fibrosis patients with and without a lung transplant in France.DOCX

BackgroundCystic fibrosis (CF) care and the life expectancy of affected patients have substantially improved in recent decades, leading to an increased number of patients being diagnosed with comorbidities, including cancers. Our objective was to characterize the epidemiology of cancers between 2006 and 2017 in CF patients with and without a lung transplant.MethodsMedical records of CF patients from 2006 to 2016 in the French CF Registry were linked to their corresponding claims data (SNDS). The annual prevalence and incidence rates of cancers were estimated from 2006 to 2017 in CF patients without lung transplant and in those with lung transplant after transplantation.ResultsOf the 7,671 patients included in the French CF Registry, 6,187 patients (80.7%) were linked to the SNDS; among them, 1,006 (16.3%) received a lung transplant. The prevalence of any cancer increased between 2006 and 2017, from 0.3 to 1.0% and from 1.3 to 6.3% in non-transplanted and transplanted patients, respectively. When compared to the general population, the incidence of cancer was significantly higher in both non-transplanted [Standardized Incidence Ratio (SIR) = 2.57, 95%CI 2.05 to 3.17] and transplanted (SIR = 19.76, 95%CI 16.45 to 23.55) patients. The median time between transplant and the first cancer was 3.9 years. Among the 211 incident cancer cases, the most frequent malignant neoplasms were skin neoplasm (48 cases), lung cancers (31 cases), gastro-intestinal (24 cases), and hematologic cancers (17 cases).ConclusionThe overall burden of cancer in CF patients is high, particularly following lung transplantation. Therefore, specific follow-up, screening and cancer prevention for CF patients with transplants are necessary.</p

PHYTOBS dataset - French National Service of Observation for Phytoplankton in coastal waters

The PHYTOBS dataset includes long-term time series on marine microphytoplankton, since 1987, along the whole French metropolitan coast. Microphytoplankton data cover microscopic taxonomic identifications and counts. The whole dataset is available, it includes 25 sampling locations.PHYTOBS network studies microphytoplankton diversity in the hydrological context along French coasts under gradients of anthropogenic pressures. PHYTOBS network allows to analyse the responses of phytoplankton communities to environmental changes, to assess the quality of the coastal environment through indicators, to define ecological niches, to detect variations in bloom phenology, and to support any scientific question by providing data.The PHYTOBS network provides the scientific community and stakeholders with validated and qualified data, in order to improve knowledge regarding biomass, abundance and composition of marine microphytoplankton in coastal and lagoon waters in their hydrological context.PHYTOBS originates of two networks. The historical REPHY (French Observation and Monitoring program for Phytoplankton and Hydrology in coastal waters) supported by Ifremer since 1984 and the SOMLIT (Service d'observation en milieu littoral) supported by INSU-CNRS since 1995. The monitoring has started in 1987 on some sites and later in others.Hydrological data are provided by REPHY or SOMLIT network as a function of site locations

Low incidence of SARS-CoV-2, risk factors of mortality and the course of illness in the French national cohort of dialysis patients

International audienceThe aim of this study was to estimate the incidence of COVID-19 disease in the French national population of dialysis patients, their course of illness and to identify the risk factors associated with mortality. Our study included all patients on dialysis recorded in the French REIN Registry in April 2020. Clinical characteristics at last follow-up and the evolution of COVID-19 illness severity over time were recorded for diagnosed cases (either suspicious clinical symptoms, characteristic signs on the chest scan or a positive reverse transcription polymerase chain reaction) for SARS-CoV-2. A total of 1,621 infected patients were reported on the REIN registry from March 16th, 2020 to May 4th, 2020. Of these, 344 died. The prevalence of COVID-19 patients varied from less than 1% to 10% between regions. The probability of being a case was higher in males, patients with diabetes, those in need of assistance for transfer or treated at a self-care unit. Dialysis at home was associated with a lower probability of being infected as was being a smoker, a former smoker, having an active malignancy, or peripheral vascular disease. Mortality in diagnosed cases (21%) was associated with the same causes as in the general population. Higher age, hypoalbuminemia and the presence of an ischemic heart disease were statistically independently associated with a higher risk of death. Being treated at a selfcare unit was associated with a lower risk. Thus, our study showed a relatively low frequency of COVID-19 among dialysis patients contrary to what might have been assumed