Éditeur(s) : Tahiti Aquaculture 2010, 6-11 décembre 2010

Droits : Tahiti Aquaculture 2010
http://archimer.ifremer.fr/doc/00063/17413/14920.pdf
http://archimer.ifremer.fr/doc/00063/17413/

Éditeur(s) : HAL CCSD Landes Bioscience
Résumé : International audience
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy

hal-00735751
https://hal.archives-ouvertes.fr/hal-00735751
PUBMED : 22966490

Éditeur(s) : HAL CCSD
Résumé : International audience
This article describes a previously unreported mutation at position 210 (C210T) of the mitochondrial large subunit ribosomal RNA (mtLSUrRNA) gene of Pneumocystis jirovecii, which led to a false-negative result of a real-time polymerase chain reaction (PCR) assay. Since the aforementioned real-time PCR assay is widely used in France, a French multicenter study was conducted to estimate the mutation frequency and its potential impact on the routine diagnosis of Pneumocystis pneumonia (PCP). Through analysis of data obtained from eight centers, the mutation frequency was estimated at 0.28%. This low frequency should not call into question the routine use of this PCR assay. Nonetheless, the occurrence of the false-negative PCR result provides arguments for maintaining microscopic techniques combined to PCR assays to achieve PCP diagnosis.
Medical Mycology

hal-01477200
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477200
DOI : 10.1093/mmy/myw051
PUBMED : 27489302

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
Previous studies in lowland tropical rainforests of French Guiana showed that, among non-N2-fixing trees, two groups of late successional species contrasting in their leaf 15N natural abundance coexist, suggesting two different main ways of nitrogen acquisition. Two abundant late-successional species typically co-occurring in rainforests in French Guiana, namely Eperua falcata and Dicorynia guianensis, were chosen as representative of each group. Stable isotope techniques and measurements of potentials of microbial N transformation were performed to assess to what extent leaf 15N natural abundance of these species could be related to (i) d15N signatures of soil mineral N sources and (ii) the capacity of soil to express nitrification and denitrification (both processes being directly involved in the balance between NH4 + and NO3 - ). Soil d15N-NH4 + was roughly similar to leaf d15N of D. guianensis (around 3.5%), suggesting a preferential use of NH4 +, whereas in E. falcata, leaf d15N values were closer to root d15N-NO3 _ values (0.2 and _2.0%, respectively), suggesting a preferential use of NO3 _. These differences in N source utilization were not accompanied by differences in availability in soil NO3 _ or in intensity of microbial functions responsible for soil N mineral evolution. However, (i) under both tree species, these functions showed clear spatial partitioning, with denitrification occurring potentially in soil and nitrification in the litter layer, and (ii) E. falcata fine roots colonized the litter layer much more strongly than D. guianensis fine roots. This strongly suggests that (i) the contrasted leaf d15N values found in the two late-successional species reveal distinct N acquisition strategies and (ii) the ability of roots to predominantly exploit the litter layer (E. falcata) or the soil (D. guianensis) may constitute an important explanation of the observed differences. A complementarity between tree species, based on mineral N resource partitioning (itself resulting from a spatially structured location of the microbial functions responsible for the balance between NH4 + and NO3 - ), can thus be supposed.
ISSN: 0038-0717

hal-01032035
https://hal.archives-ouvertes.fr/hal-01032035
DOI : 10.1016/j.soilbio.2007.09.011

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Iron is an essential micronutrient involved in many biological processes and is often limiting for primary production in large regions of the World Ocean. Metagenomic and physiological studies have identified clades or ecotypes of marine phytoplankton that are specialized in iron depleted ecological niches. Although less studied, eukaryotic picophytoplankton does contribute significantly to primary production and carbon transfer to higher trophic levels. In particular, metagenomic studies of the green picoalga Ostreococcus have revealed the occurrence of two main clades distributed along coast-offshore gradients, suggesting niche partitioning in different nutrient regimes. Here, we present a study of the response to iron limitation of four Ostreococcus strains isolated from contrasted environments. Whereas the strains isolated in nutrient-rich waters showed high iron requirements, the oceanic strains could cope with lower iron concentrations. The RCC802 strain, in particular, was able to maintain high growth rate at low iron levels. Together physiological and transcriptomic data indicate that the competitiveness of RCC802 under iron limitation is related to a lowering of iron needs though a reduction of the photosynthetic machinery and of protein content, rather than to cell size reduction. Our results overall suggest that iron is one of the factors driving the differentiation of physiologically specialized Ostreococcus strains in the ocean.
ISSN: 2045-2322

Droits : http://creativecommons.org/licenses/by/
hal-01502140
http://hal.upmc.fr/hal-01502140
http://hal.upmc.fr/hal-01502140/document
http://hal.upmc.fr/hal-01502140/file/acclimation.pdf
DOI : 10.1038/s41598-017-00216-6

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The purpose of this investigation was to characterize the management and prognosis of severe Pneumocystis jirovecii pneumonia (PJP) in human immunodeficiency virus (HIV)-negative patients. An observational cohort study of HIV-negative adults with PJP documented by bronchoalveolar lavage (BAL) through Gomori-Grocott staining or immunofluorescence, admitted to one intensive care unit (ICU) for acute respiratory failure, was undertaken. From 1990 to 2010, 70 patients (24 females, 46 males) were included, with a mean age of 58.6 ± 18.3 years. The mean Simplified Acute Physiology Score (SAPS)-II was 36.9 ± 20.4. Underlying conditions included hematologic malignancies (n = 21), vasculitis (n = 13), and solid tumors (n = 13). Most patients were receiving systemic corticosteroids (n = 63) and cytotoxic drugs (n = 51). Not a single patient received trimethoprim-sulfamethoxazole as PJP prophylaxis. Endotracheal intubation (ETI) was required in 42 patients (60.0 %), including 38 with acute respiratory distress syndrome (ARDS). In-ICU mortality was 52.9 % overall, reaching 80.9 % and 86.8 %, respectively, for patients who required ETI and for patients with ARDS. In the univariate analysis, in-ICU mortality was associated with SAPS-II (p = 0.0131), ARDS (p < 0.0001), shock (p < 0.0001), and herpes simplex virus (HSV) or cytomegalovirus (CMV) on BAL (p = 0.0031). In the multivariate analysis, only ARDS was associated with in-ICU mortality (odds ratio [OR] 23.4 [4.5-121.9], p < 0.0001). PJP in non-HIV patients remains a serious disease with high in-hospital mortality. Pulmonary co-infection with HSV or CMV may contribute to fatal outcome.
ISSN: 0934-9723

inserm-00872789
http://www.hal.inserm.fr/inserm-00872789
DOI : 10.1007/s10096-012-1730-7
PUBMED : 22930407

Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : International audience
This study provides a baseline describing natural small scale variability of Symbiodinium density in the sentinel coral Acropora globiceps during the summer, under non-bleaching conditions. Spatial scales investigated range from the colony scale (1-10 cm, i.e. among branches of the same colony) to the reef scale (1-10 km, i.e. among stations distributed over several locations and depths), at Moorea Island, French Polynesia. The coral-Symbiodinium symbiosis is a key process in scleractinian coral physiology, and Symbiodinium density provides an easy-to-measure and inexpensive biomarker of this symbiosis health. Spatial variability of three major environmental factors: light intensity, sedimentation and water motion was also assessed to evaluate their potential link with Symbiodinium density. Density of Symbiodinium did not significantly differ within colonies or among colonies within a station. However, a marked depth gradient was observed, showing increasing density with increasing depth and decreasing light intensity. These observations provide an interesting reference for forthcoming comparisons with disturbed conditions, such as bleaching events.
ISSN: 0025-3154

hal-00905942
https://hal.archives-ouvertes.fr/hal-00905942
https://hal.archives-ouvertes.fr/hal-00905942/document
https://hal.archives-ouvertes.fr/hal-00905942/file/Ladriereetal2014.pdf
DOI : 10.1017/S0025315413001252

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 [Commercial Publisher]
Résumé : International audience
BACKGROUND: Pneumocystis jiroveci pneumonia in HIV-negative immunocompromised patients is associated with high mortality rates. Although trimethoprim-sulfamethoxazole (TMP-SMX) provides a very effective prophylaxis, pneumocystosis still occurs and may even be emerging, due to sub-optimal characterization of patients most at risk, hence precluding targeted prophylaxis. METHODS: We retrospectively analyzed all cases of documented pneumocystosis in HIV-negative patients admitted in our institution, a referral center in the area, from January 1990 to June 2010, and extracted data on their underlying condition(s). To estimate incidence rates within each condition, we estimated the number of patients followed-up in our area for each condition, by measuring the number of patients admitted with the corresponding international classification diagnostic code, through the national hospital discharge database (PMSI). RESULTS: From 1990 to 2010, 293 cases of pneumocystosis were documented, of whom 154 (52.6%) tested negative for HIV. The main underlying conditions were hematological malignancies (32.5%), solid tumors (18.2%), inflammatory diseases (14.9%), solid organ transplant (12.3%), and vasculitis (9.7%). Estimated incidence rates could be ranked in three categories: i) high risk (incidence rates extgreater 45 cases per 100,000 patient-year): polyarteritis nodosa, granulomatosis with polyangiitis, polymyositis/dermatopolymyositis, acute leukemia, chronic lymphocytic leukemia, and non-Hodgkin lymphoma; ii) intermediate risk (25-45 cases per 100,000 patient-year): Waldenström macroglobulinemia, multiple myeloma, and central nervous system cancer; and iii) low risk ( extless 25 cases per 100,000 patient-year): other solid tumors, inflammatory diseases, and Hodgkin lymphoma. CONCLUSIONS: These estimates may be used as a guide to better target pneumocystosis prophylaxis in the groups most at risk.
ISSN: 0002-9343

hal-01063911
https://hal.archives-ouvertes.fr/hal-01063911
https://hal.archives-ouvertes.fr/hal-01063911/document
https://hal.archives-ouvertes.fr/hal-01063911/file/1-s2.0-S0002934314005907-main.pdf
DOI : 10.1016/j.amjmed.2014.07.010

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 American Society for Microbiology
Résumé : International audience
Pneumocystis jirovecii pneumonia (PCP) is a life-threatening infection in immunocompromised patients. Quantitative real-time PCR (qPCR) is more sensitive than microscopic examination for the detection of P. jirovecii but also detects colonized patients. Hence, its positive predictive value (PPV) needs evaluation. In this 4-year prospective observational study, all immunocompromised patients with acute respiratory symptoms who were investigated for PCP were included, totaling 659 patients (814 bronchoalveolar lavage fluid samples). Patients with negative microscopy but positive qPCR were classified through medical chart review as having retained PCP, possible PCP, or colonization, and their clinical outcomes were compared to those of patients with microscopically proven PCP. Overall, 119 patients were included for analysis, of whom 35, 41, and 43 were classified as having retained PCP, possible PCP, and colonization, respectively. The 35 patients with retained PCP had clinical findings similar to those with microscopically proven PCP but lower fungal loads (P extless 0.001) and were mainly non-HIV-infected patients (P extless 0.05). Although the mean amplification threshold was higher in colonized patients, it was not possible to determine a discriminant qPCR cutoff. The PPV of qPCR in patients with negative microscopy were 29.4% and 63.8% when considering retained PCP and retained plus possible PCP, respectively. Patients with possible PCP had a higher mortality rate than patients with retained PCP or colonization (63% versus 3% and 16%, respectively); patients who died had not received co-trimoxazole. In conclusion, qPCR is a useful tool to diagnose PCP in non-HIV patients, and treatment might be better targeted through a multicomponent algorithm including both clinical/radiological parameters and qPCR results.
ISSN: 0095-1137

hal-01063906
https://hal.archives-ouvertes.fr/hal-01063906
DOI : 10.1128/JCM.01480-14
PUBMED : 25009050