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Tissue-specific bioaccumulation of a wide range of legacy and emerging persistent organic contaminants in swordfish (Xiphias gladius) from Seychelles, Western Indian Ocean
No full textSwordfish (Xiphias gladius) is a major marine resource of high economic value to industrial and artisanal fisheries. As a top predator with a long lifespan, it is prone to accumulate high levels of contaminants. The bioaccumulation of a wide range of both legacy and emerging persistent organic contaminants was investigated in the muscle, liver and gonads of swordfish collected from the Seychelles, western Indian Ocean. The detection of all target contaminants, some at frequencies above 80%, highlights their widespread occurrence, albeit at low levels. Mean concentrations in muscle were 5637, 491 and 331 pg g(-1) ww for organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs) and perfluoroalkyl substances (PFASs), respectively. XBFR mean concentrations were far below, i.e. 47 pg g(-1) ww. The data are among the first obtained for such a high diversity of contaminants in an oceanic top predator worldwide and constitute a benchmark of the contamination of Indian Ocean ecosystems
Outcomes of second-line antiretroviral therapy among children living with HIV : a global cohort analysis
No full textIntroduction : Limited data describe outcomes on second-line antiretroviral therapy (ART) among children globally. Our objective was to contribute data on outcomes among children living with HIV after initiation of second-line ART in the context of routine care within a large global cohort collaboration. Methods : Patient-level data from 1993 through 2015 from 11 paediatric HIV cohorts were pooled. Characteristics at switch and through two years of follow-up were summarized for children who switched to second-line ART after starting a standard first-line regimen in North America, Latin America, Europe, Asia, Southern Africa (South Africa & Botswana) and the rest of sub-Saharan Africa (SSA). Cumulative incidences of mortality and loss to follow-up (LTFU) were estimated using a competing risks framework. Results : Of the 85,389 children on first-line ART, 3,555 (4%) switched to second-line after a median of 2.8 years on ART (IQR: 1.6, 4.7); 69% were from Southern Africa or SSA and 86% of second-line regimens were protease inhibitor-based. At switch, median age was 8.4 years and 50% had a prior AIDS diagnosis. Median follow-up after switch to second-line ranged from 1.8 years in SSA to 5.3 years in North America. Median CD4 counts at switch to second-line ranged from 235 cells/mm(3) in SSA to 828 cells/mm(3) in North America. Improvements in CD4 counts were observed over two years of follow-up, particularly in regions with lower CD4 counts at second-line switch. Improvements in weight-for-age z-scores were not observed during follow-up. Cumulative incidence of LTFU at two years was <5% in all regions except SSA (7.1%) and Southern Africa (7.4%). Risk of mortality was <3% at two years of follow-up in all regions, except Latin America (4.9%) and SSA (5.5%). Conclusions : Children switched to second-line ART experience CD4 count increases as well as low to moderate rates of LTFU and mortality within two years after switch. Severe immune deficiency at time of switch in some settings suggests need for improved recognition and management of treatment failure in children
Multiplex detection and dynamics of IgG antibodies to SARS-CoV2 and the highly pathogenic human coronaviruses SARS-CoV and MERS-CoV
No full textBackground: Knowledge of the COVID-19 epidemic extent and the level of herd immunity is urgently needed to help manage this pandemic. Methods: We used a panel of 167 samples (77 pre-epidemic and 90 COVID-19 seroconverters) and SARS-CoV1, SARS-CoV2 and MERS-CoV Spike and/or Nucleopcapsid (NC) proteins to develop a high throughput multiplex screening assay to detect IgG antibodies in human plasma. Assay performances were determined by ROC curves analysis. A subset of the COVID-19+ samples (n= 36) were also tested by a commercial NC-based ELISA test and the results compared with those of the novel assay. Results: On samples collected >= 14 days after symptoms onset, the accuracy of the assay is 100 % (95 % CI: 100-100) for the Spike antigen and 99.9 % (95 % CI:99.7-100) for NC. By logistic regression, we estimated that 50 % of the patients have seroconverted at 5.7 +/- 1.6; 5.7 +/- 1.8 and 7.9 +/- 1.0 days after symptoms onset against Spike, NC or both antigens, respectively and all have seroconverted two weeks after symptoms onset. IgG titration in a subset of samples showed that early phase samples present lower IgG titers than those from later phase. IgG to SARS-CoV2 NC cross-reacted at 100 % with SARS-CoV1 NC. Twenty-nine of the 36 (80.5 %) samples tested were positive by the commercial ELISA while 31/36 (86.1 %) were positive by the novel assay. Conclusions: Our assay is highly sensitive and specific for the detection of IgG antibodies to SARS-CoV2 proteins, suitable for high throughput epidemiological surveys. The novel assay is more sensitive than a commercial ELISA
Citizen Science, a promising tool for detecting and monitoring outbreaks of the crown-of-thorns starfish Acanthaster spp.
No full textMonitoring potentially devastating coral-eating crown-of-thorns starfish (COTS) populations at scales relevant to management is a challenging task. Here, we investigated a citizen science approach to detect COTS outbreaks and prioritize management responses. Between 2014 and 2018, 38 000 COTS were recorded through 641 online observation reports submitted across New Caledonia, Vanuatu and Fiji by private stakeholders (51%), NGOs (22%), business operator (11%), research/government agencies (16%). COTS were observed in multiple areas, including in remote/inhabited reefs where they had never been reported. A three-level classification was developed to discriminate risk areas and propose operational guidelines to streamline management actions. About two-thirds of reports had low abundances (<10 starfish sighted) and could be addressed with low priority. Verification surveys at 65 reef sites confirmed outbreaks in half of the cases, along with high peak densities (7 000 ind.ha(-1)). Combining professional and non-professional observers increased the detection range (+27%) and the number of COTS detections (+129%). Citizen reports were eventually followed by removal campaigns organized within diverse institutional frameworks. While citizen monitoring has intrinsic limitations, we advocate that it constitutes a complementary and promising approach to support the ongoing management efforts in all countries affected by COTS
Primary production and depth drive different trophic structure and functioning of fish assemblages in French marine ecosystems
No full textInvestigating the drivers of fish assemblage trophic structure is a critical question, in order to better understand ecosystem functioning, predict the effects of perturbations and implement integrated management of exploited marine ecosystems. Ecosystemic surveys enabled the determination of the trophic structure of the fish assemblages in three French marine ecosystems, namely the Eastern English Channel, the Bay of Biscay and the Gulf of Lions, through the simultaneous collection of qualitative (stable isotopes and energy content) and quantitative (biomass) data. In the Bay of Biscay and in the Gulf of Lions, pelagic primary production supported at least 80% of the fish biomass production, and explained the dominance of pelagic species, but with differences resulting from the different productivity. The lower productivity in the oligotrophic Gulf of Lions led to a lower total biomass, energy density as well as the predominance of zooplankton-feeders. In contrast, fluxes in the Bay of Biscay were sufficient to support a higher biomass of pelagic piscivores, and of species with higher energy content. In the shallow Eastern English Channel, the respective contributions of pelagic and benthic sources were similar. Bentho-demersal species of higher trophic level dominated this assemblage, because of their ability to exploit both pathways. Results of the present study confirmed that fisheries-focused surveys can be used as efficient platforms to address questions about ecosystem functioning. Here, it confirmed the expected differences between ecosystems and the importance of primary production and environment as drivers of fish assemblage structure and functioning. Future studies should nevertheless develop new methods to better assess the paramount role of low trophic level consumers
Zoonotic Abbreviata caucasica in wild chimpanzees (Pan troglodytes verus) from Senegal
No full textAbbreviata caucasica (syn.Physaloptera mordens) has been reported in human and various non-human primates including great apes. The identification of this nematode is seldom performed and relies on egg characterization at the coproscopy, in the absence of any molecular tool. Following the recovery of two adult females ofA. caucasicafrom the feces of wild Senegalese chimpanzees, morphometric characteristics were reported and new data on the width of the esophagus (0.268-0.287 mm) and on the cuticle structure (0.70-0.122 mm) were provided. The molecular characterization of a set of mitochondrial (cox1, 16S rRNA, 12S rRNA) and nuclear (18S rRNA and ITS2) partial genes was performed. Our phylogenetic analysis indicates for the first time thatA. caucasicais monophyletic withPhysalopteraspecies. A novel molecular tool was developed for the routine diagnosis ofA. caucasicaand the surveillance of Nematoda infestations. An A. caucasica-specific qPCR targeting the 12S gene was assessed. The assay was able to detect up to 1.13 x 10(-3)eggs/g of fecal matter irrespective of its consistency, with an efficiency of 101.8% and a perfect adjustment (R-2= 0.99). The infection rate byA. caucasicain the chimpanzee fecal samples was 52.08%. Only 6.19% of the environmental samples were positive for nematode DNA and any forA. caucasica. Our findings indicate the need for further studies to clarify the epidemiology, circulation, life cycle, and possible pathological effects of this infestation using the molecular tool herein developed
Evaluation and calibration of alternative methods for estimating reference evapotranspiration in the Senegal River Basin
No full textReference evapotranspiration (ET0) is a key element of the water cycle in tropical areas for the planning and management of water resources, hydrological modeling, and irrigation management. The objective of this research is to assess twenty methods in computing ET0 in the Senegal River Basin and to calibrate and validate the best methods that integrate fewer climate variables. The performance of alternative methods compared to the Penman Monteith (FAO56-PM) model is evaluated using the coefficient of determination (R-2), normalized root mean square error (NRMSE), percentage of bias (PBIAS), and the Kling-Gupta Efficiency (KGE). The most robust methods integrating fewer climate variables were calibrated and validated and the results show that Trabert, Valiantzas 2, Valiantzas 3, and Hargreaves and Samani models are, respectively, the most robust for ET0 estimation. The calibration improves the estimates of reference evapotranspiration compared to original models. It improved the performance of these models with an increase in KGE values of 45%, 32%, 29%, and 19% for Trabert, Valiantzas 2, Valiantzas 3, and Hargreaves and Samani models, respectively. From a spatial point of view, the calibrated models of Trabert and Valiantzas 2 are robust in all the climatic zones of the Senegal River Basin, whereas, those of Valiantzas 3 and Hargreaves and Samani are more efficient in the Guinean zone. This study provides information on the choice of a model for estimating evapotranspiration in the Senegal River Basin
Bio-physical coupling around three shallow seamounts in the South Western Indian Ocean, with regional comparisons based on modelling, remote sensing and observational studies
No full textCompared with other ocean basins, little is known scientifically about the seamounts in the Indian Ocean. Nonetheless, fishers have plundered these fragile ecosystems for decades, and now mining is becoming a reality. We introduce a multidisciplinary project referred to as MAD-Ridge that recently focused on three shallow seamounts in the South West Indian Ocean between 19 degrees S and 34 degrees S. The larger Walters Shoal (summit at 18 m) discovered in 1963 occupies the southern part of the Madagascar Ridge and has long received attention from the fishing industry, and only recently by scientists. In contrast, nothing is known of the northern region of the ridge, which is characterised by a prominent, steep-sided seamount that has a flat circular summit at 240 m and width of similar to 20 km. This seamount is some 200 km south of Madagascar and unnamed; it is referred to here as the MAD-Ridge seamount. MAD-Ridge is the shallowest of a constellation of five deeper (>1200 m) seamounts on that part of the ridge, all within the EEZ of Madagascar. It lies in a highly dynamic region at the end of the East Madagascar Current, where mesoscale eddies are produced continuously, typically as dipoles. The Madagascar Ridge appears to be an area of great productivity, as suggested by the foraging behaviour of some tropical seabirds during chick-rearing and a longline fishery that operates there. The third seamount, La Perouse, is located between Reunion Island and Madagascar. With a summit 60 m below the sea surface, La Perouse is distinct from MAD-Ridge and Walters Shoal; it is a solitary pinnacle surrounded by deep abyssal plains and positioned in an oligotrophic region with low mesoscale activities. The overall aim of the MAD-Ridge project was to examine the flow structures induced by the abrupt topographies, and to evaluate whether biological responses could be detected that better explain the observed increased in fish and top predator biomasses. The MAD-Ridge project comprised a multidisciplinary team of senior and early career scientists, along with postgraduate students from France, South Africa, Mauritius and Madagascar. The investigation was based around three cruises using the French vessels RV Antea (35 m) and RV Marion Dufresne (120 m) in September 2016 (La Perouse), November-December 2016 (MAD-Ridge) and May 2017 (Walters Shoal). This manuscript presents the rationale for the MAD-Ridge project, the background, a description of the research approach including the cruises, and a synopsis of the results gathered in the papers published in this Special Issue
Sub-oxycline methane oxidation can fully uptake CH4 produced in sediments : case study of a lake in Siberia
No full textIt is commonly assumed that methane (CH4) released by lakes into the atmosphere is mainly produced in anoxic sediment and transported by diffusion or ebullition through the water column to the surface of the lake. In contrast to that prevailing idea, it has been gradually established that the epilimnetic CH4 does not originate exclusively from sediments but is also locally produced or laterally transported from the littoral zone. Therefore, CH4 cycling in the epilimnion and the hypolimnion might not be as closely linked as previously thought. We utilized a high-resolution method used to determine dissolved CH4 concentration to analyze a Siberian lake in which epilimnetic and hypolimnetic CH4 cycles were fully segregated by a section of the water column where CH4 was not detected. This layer, with no detected CH4, was well below the oxycline and the photic zone and thus assumed to be anaerobic. However, on the basis of a diffusion-reaction model, molecular biology, and stable isotope analyses, we determined that this layer takes up all the CH4 produced in the sediments and the deepest section of the hypolimnion. We concluded that there was no CH4 exchange between the hypolimnion (dominated by methanotrophy and methanogenesis) and the epilimnion (dominated by methane lateral transport and/or oxic production), resulting in a vertically segregated lake internal CH4 cycle
Bio-physical coupling around three shallow seamounts in the South Western Indian Ocean, with regional comparisons based on modelling, remote sensing and observational studies
No full textThis work is part of the MADRidge Project special issue which aims to describe pelagic ecosystems in the vicinity of three prominent shallow seamounts in the South West Indian Ocean: one here named MAD-Ridge (240 m below the surface) plus Walters Shoal (18 m) on the Madagascar Ridge, and La Perouse (60 m) on the abyssal plain east of Madagascar. The three span latitudes 20 degrees S and 33 degrees S, some 1500 km. The study provides the background oceanography for the once-off, multidisciplinary snapshot cruise studies around the seamounts. As life on seamounts is determined by factors such as summit depth, proximity to the light layers of the ocean, and the ambient circulation, a first description of regional spatial-field climatologies (16-22 years) and monthly along-ridge gradients of surface wind (driving force), water column properties of sea surface temperature, mixed layer depth, chlorophyll-a and eddy kinetic energy, plus ocean currents is provided. Being relevant to many applications in the study domain, these properties in particular reveal contrasting environments along the Madagascar Ridge and between the three seamounts that should drive biological differences. Relative to the other two seamounts, MAD-Ridge is in the more extreme situation, being at the end of the East Madagascar Current, where it experiences sturdy, albeit variable, currents and the frequent passing of mesoscale eddies