Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq), transcriptome analyses, and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1) transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata, and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the crossroads between redox homeostasis, oxygen consumption, and iron metabolism.
ISSN: 1664-302X

Droits : http://creativecommons.org/licenses/by/
hal-01323791
http://hal.upmc.fr/hal-01323791
http://hal.upmc.fr/hal-01323791/document
http://hal.upmc.fr/hal-01323791/file/fmicb-07-00645.pdf
DOI : 10.3389/fmicb.2016.00645

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
ISSN: 1462-2912

hal-01191731
http://hal.upmc.fr/hal-01191731
http://hal.upmc.fr/hal-01191731/document
http://hal.upmc.fr/hal-01191731/file/Massana_2015_Marine_protist.pdf
DOI : 10.1111/1462-2920.12955

Éditeur(s) : HAL CCSD American Medical Association (AMA)
Résumé : International audience
IMPORTANCE Although frequently used in treating intensive care unit (ICU) patients with sepsis, empirical antifungal therapy, initiated for suspected fungal infection, has not been shown to improve outcome. OBJECTIVE To determine whether empirical micafungin reduces invasive fungal infection (IFI)-free survival at day 28. DESIGN, SETTING, AND PARTICIPANTS Multicenter double-blind placebo-controlled study of 260 nonneutropenic, nontransplanted, critically ill patients with ICU-acquired sepsis, multiple Candida colonization, multiple organ failure, exposed to broad-spectrum antibacterial agents, and enrolled between July 2012 and February 2015 in 19 French ICUs. INTERVENTIONS Empirical treatment with micafungin (100mg, once daily, for 14 days) (n = 131) vs placebo (n = 129). MAIN OUTCOMES AND MEASURES The primary end pointwas survival without proven IFI 28 days after randomization. Key secondary end points included new proven fungal infections, survival at day 28 and day 90, organ failure, serum (1-3)-beta-D-glucan level evolution, and incidence of ventilator-associated bacterial pneumonia. RESULTS Among 260 patients (mean age 63 years; 91 [35%] women), 251 (128, micafungin group; 123, placebo group) were included in the modified intent-to-treat analysis. Median values were 8 for Sequential Organ Failure Assessment (SOFA) score, 3 for number of Candida-colonized sites, and 99 pg/mL for level of (1-3)-beta-D-glucan. On day 28, there were 82 (68%) patients in the micafungin group vs 79 (60.2%) in the placebo group who were alive and IFI free (hazard ratio [HR], 1.35 [95% CI, 0.87-2.08]). Results were similar among patients with a (1-3)-beta-D-glucan level of greater than 80 pg/mL (n = 175; HR, 1.41 [95% CI, 0.85-2.33]). Day-28 IFI-free survival in patients with a high SOFA score (> 8) was not significantly different when compared between the micafungin vs placebo groups (HR, 1.69 [95% CI, 0.96-2.94]). Use of empirical micafungin decreased the rate of new invasive fungal infection in 4 of 128 patients (3%) in the micafungin group vs placebo (15/123 patients [12%]) (P =.008). CONCLUSIONS AND RELEVANCE Among nonneutropenic critically ill patients with ICU-acquired sepsis, Candida species colonization at multiple sites, and multiple organ failure, empirical treatment with micafungin, compared with placebo, did not increase fungal infection-free survival at day 28.
ISSN: 0098-7484

hal-01405822
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01405822
DOI : 10.1001/jama.2016.14655
PUBMED : 27706483

Éditeur(s) : HAL CCSD
Résumé : International audience
Background: Mounier-Kuhn syndrome (MKS) is a rare disorder characterized by enlargement of the trachea and main bronchi and associated with recurrent respiratory tract infections. Objective: This multicenter, retrospective study was carried out to describe respiratory conditions associated with tracheobronchomegaly. Methods: Nine institutions involved in the ‘Groupe d'Endoscopie de Langue Française' (GELF) participated in this study. A standard form was used to record patient characteristics, treatments and follow-up from medical charts. Results: Seventeen patients, 53% male, aged 58 ± 18 years at diagnosis were included. Recurrent infections revealed MKS in 88% of cases. Main comorbid conditions were diffuse bronchiectasis in 88% of patients and tracheobronchomalacia in 67% of cases. The exacerbation rate was 1.5 exacerbations/patient/year. The main non-respiratory morbid condition was gastroesophageal reflux disease in 29% of cases. Interventional bronchoscopy was performed in seven patients (41%), consisting of laser (n = 2) and tracheal stenting (n = 5). Complications related to stents were observed in 80% of cases with a mean stent duration of 8 months. Four deaths, including three due to respiratory causes, occurred during follow-up. Conclusions: This is the largest series of MKS reported in the literature, showing that bronchiectasis and tracheobronchomalacia are the main associated morbid conditions that constitute a challenge for treatment.
Respiration

hal-01331182
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01331182
DOI : 10.1159/000445029
PUBMED : 27022925

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
ISSN: 0305-7453

hal-01470808
https://hal.archives-ouvertes.fr/hal-01470808
DOI : 10.1093/jac/dkw352
PUBMED : 27609051

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : We use InSAR to measure deformation and kinematics of the Mw = 4.9 Borujerd (2005/05/03) and Mw = 6.1 Chalan-Chulan (2006/03/31) earthquakes that occurred in the Zagros fold-and-thrust belt. The focal mechanism of the 2006 event is consistent with right lateral strike-slip motion and the event ruptured the Dorud-Borujerd segment of the Main Recent Fault. An Envisat interferogram spanning the 2006 event shows peak ground deformation of 9 cm in the satellite line-of-sight along a 10 km long fault portion. The interferogram spanning the 2005 earthquake is rather related to atmospheric artefact than to ground deformation. Dislocation models of the 2006 Chalan-Chulan event indicate dextral slip amounting to a maximum of 90 cm at a depth of 4 km. The predicted vertical displacements are in good agreement with differential levelling data. The 2006 event filled only a small part of the seismic gap located between large M = 7 events that occurred in 1909 and 1957.
ISSN: 0954-4879

hal-00411313
https://hal.archives-ouvertes.fr/hal-00411313
DOI : 10.1111/j.1365-3121.2008.00797.x

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
ISSN: 1755-098X

hal-01149047
http://hal.upmc.fr/hal-01149047
http://hal.upmc.fr/hal-01149047/document
http://hal.upmc.fr/hal-01149047/file/Decelle_2015_PhytoREF.pdf
DOI : 10.1111/1755-0998.12401

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
In Taiwan, about one third of the lithospheric plate convergence between Eurasia and the Philippine Sea plate is accommodated on the eastern coast across the narrow Longitudinal Valley (LV). The Longitudinal Valley Fault (LVF) is the main seismically active fault zone in this region. However, the spatial distribution of ground deformation due to interseismic loading on locked fault segments remains widely unknown. To address this problem, we use a "permanent scatterer" (PS) interferometric synthetic aperture radar (InSAR) approach for processing the ERS satellite archives. The PS mean velocity maps allow accurately mapping and quantifying the ground deformation all along the LV. Assuming that, close to the surface, the fault plane along the central LVF creeping segment dips 55 degrees to the east, we derive a slip vector at the surface of similar to 25 mm/yr with a mean rake of 70 degrees. In agreement with our PS observations, shallow seismicity indicates a clear change in the fault mechanical behavior of the creeping segment around Fuli town. Finally, we propose a combination of the PS velocity fields for estimating a 3-D map of ground deformation. In the southern part of the LV, the vertical component reveals an uplift of the Coastal Range with respect to the LV of similar to 10 mm/yr. Moreover, between Taitung and Luyeh, the vertical deformation is essentially accommodated along the Luyeh Strand. Finally, north of Rueisuei, the Coastal Range uniformly subsides at similar to 15 mm/yr relative to the western side of the LV. However, a local uplift pattern is detected around latitude 23 degrees 42'.
ISSN: 0148-0227

hal-00595532
https://hal.archives-ouvertes.fr/hal-00595532
DOI : 10.1029/2010JB007898

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
OBJECTIVES: Tracheobronchial stenosis (TBS) is noted in 12-23% of patients with granulomatosis with polyangiitis (GPA), and includes subglottic stenosis and bronchial stenosis. We aimed to analyse the endoscopic management of TBS in GPA and to identify factors associated with the efficacy of endoscopic interventions. METHODS: We conducted a French nationwide retrospective study that included 47 patients with GPA-related TBS. RESULTS: Compared with patients without TBS, those with TBS were younger, more frequently female and had less frequent kidney, ocular and gastrointestinal involvement and mononeuritis multiplex. Endoscopic procedures included 137 tracheal and 50 bronchial interventions, mainly endoscopic dilatation, local steroid injection and conservative laser surgery, and less frequently stenting. After the first endoscopic procedure, the cumulative incidence of endoscopic treatment failure was 49% at 1 year, 70% at 2 years and 80% at 5 years. Factors significantly associated with a higher cumulative incidence of treatment failure were a shorter time from GPA diagnosis to endoscopic procedure [hazard ratio (HR) 1.08 (95% CI 1.01, 1.14); P = 0.01] and a bronchial stenosis [HR 1.96 (95% CI 1.28, 3.00); P = 0.002]. A prednisone dose ≥30 mg/day at the time of the procedure was associated with a lower cumulative incidence of treatment failure [HR 0.53 (95% CI 0.31, 0.89); P = 0.02]. CONCLUSION: TBS represents severe and refractory manifestations with a high rate of restenosis. High-dose systemic CSs at the time of the procedure and increased time from GPA diagnosis to bronchoscopic intervention are associated with a better event-free survival. In contrast, bronchial stenoses are associated with a higher rate of restenosis than subglottic stenosis.
ISSN: 1462-0324

hal-01155105
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01155105
DOI : 10.1093/rheumatology/kev129
PUBMED : 26001634

Éditeur(s) : HAL CCSD Wiley
Résumé : While attention on logging in the tropics has been increasing, studies on the long-term effects of silviculture on forest dynamics and ecology remain scare and spatially limited. Indeed, most of our knowledge on tropical forests arises from studies carried out in undisturbed tropical forests. This bias is problematic given that logged and disturbed tropical forests are now covering a larger area than the so-called primary forests. A new network of permanent sample plots in logged forests, the Tropical managed Forests Observatory (TmFO), aims to fill this gap by providing unprecedented opportunities to examine long-term data on the resilience of logged tropical forests at regional and global scales. TmFO currently includes 24 experimental sites distributed across three tropical regions, with a total of 490 permanent plots and 921ha of forest inventories.
ISSN: 1402-2001

hal-01204230
https://hal.archives-ouvertes.fr/hal-01204230
DOI : 10.1111/avsc.12125
PRODINRA : 323838

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Northwest Iran is characterized by a high level of historical and instrumental seismicity related to the ongoing convergence between the Arabian and Eurasian plates. In this region, the main right-lateral strike-slip fault known as the North Tabriz fault (NTF) forms the central portion of a large crustal fault system called the Tabriz fault system (TFS). The NTF is a major seismic source along which at least three strong and destructive earthquakes have occurred since 858 AD. The two most recent destructive seismic events occurred in 1721 AD and 1780 AD, rupturing the SE and NW fault segments, respectively. This paper reports paleoseismological and quantitative geomorphologic investigations on the SE segment of the NTF, between the cities of Bostanabad and Tabriz. These observations help to improve our understanding of the seismic hazard for Tabriz city and its surrounding areas. Our field investigations revealed evidence of successive faulting events since the Late Quaternary. Paleoseismic investigations indicate that since 33.5 kyr, the SE segment of the NTF has experienced at least three major (M>7.5) seismic events, including the 1721 AD earthquake (M=7.6–7.7). Along the NW segment of the fault, however, our results suggest that the amount of strong (M~7.5) seismic events during the same period is significantly greater than along the SE segment. One possible explanation of such a difference in seismic activity is that the Late Quaternary-Holocene coseismic slip rate is decreasing along the NTF from the northwest to the southeast. This explanation contradicts the former hypothesis of a constant slip rate along the whole length of the NTF. In addition, more distributed deformation along several parallel fault branches, in a wider fault zone of the SE segment of the NTF may be considered as additional evidence for the estimation of lower rate of deformation along the fault segment. Such a slip distribution pattern can explain the existence of smaller (~300 m) Pliocene-Quaternary cumulative dextral offsets along the SE fault segment than the measured cumulative offsets along the NW segment (~800 m) of the NTF.
ISSN: 0040-1951

hal-01089420
http://hal.upmc.fr/hal-01089420
http://hal.upmc.fr/hal-01089420/document
http://hal.upmc.fr/hal-01089420/file/Solaymani%20Azad%20et%20al.%2C%202014%20%28accepted%29.pdf
DOI : 10.1016/j.tecto.2014.11.010