A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.     

Spontaneous Reperfusion after In Situ Thromboembolic Stroke in Mice

Injection of thrombin into the middle cerebral artery (MCA) of mice has been proposed as a new model of thromboembolic stroke. The present study used sequential multiparametric Magnetic Resonance Imaging (MRI), including Magnetic Resonance Angiography (MRA), Diffusion-Weighted Imaging (DWI) and Perfusion-Weighted Imaging (PWI), to document MCA occlusion, PWI-DWI mismatch, and lesion development. In the first experiment, complete MCA occlusion and reproducible hypoperfusion were obtained in 85% of animals during the first hour after stroke onset. In the second experiment, 80% of animals showed partial to complete reperfusion during a three-hour follow-up. Spontaneous reperfusion thus contributed to the variability in ischemic volume in this model. The study confirmed the value of the model for evaluating new thrombolytic treatments, but calls for extended MRI follow-up at the acute stage in therapeutic studies.     

Tolerance of young allis shad Alosa alosa (Clupeidae) to oxy-thermic stress

The ecology of the young stages of allis shad Alosa alosa is poorly documented, although they can be exposed to many pressures during their freshwater phase and their downstream migration. When passing through systems such as the Gironde-Garonne-Dordogne watershed (GGD, SW France), they can be subjected to high temperatures and low levels of oxygen (hypoxia). The aim of this work is to assess the tolerance of young Alosa alosa at four ages (c. 10, 30, 60 and 85 days old) by challenging them to different temperatures (18, 22, 26 and 28°C) together with decreasing oxygen saturation levels (from 100% to 30%). Survival of the 10-day-old individuals was not influenced by oxy-thermic conditions, but high stress levels were detected and perhaps this age class was too fragile regarding the constraint of the experimental design. Survival at 30 and at 60 days old was negatively influenced by the highest temperatures tested alone (from 26°C and from 28°C, respectively) but no effect was detected at 85 days old up to 28°C. A combined effect of temperature and oxygen level was highlighted, with heat accelerating survival decrease when associated with oxygen level depletion: essentially, survival was critical (<50%) at 30 days old at temperature ≥22°C together with 30% O₂; at 60 days old, at temperature = 28°C with 30% O₂; at 85 days old, at temperature ≥26°C with ≤40% O₂. Tolerance to oxy-thermic pressures appeared to be greater among the migratory ages (60 and 85 days old) than among the 30-day-old group. Based on environmental data recorded in the GGD system and on our experimental results, an exploratory analysis allowed a discussion of the possible impact of past oxy-thermic conditions on the local population dynamics between 2005 and 2018. The oxy-thermic conditions that may affect Alosa alosa at ages when they migrate downstream (60 and 85 days old) were not frequently recorded in this period, except in cases of extreme episodes of heat together with hypoxia that occurred in some years, in summertime in the turbidity maximum zone of the Gironde estuary (particularly in the year 2006). Interestingly, oxy-thermic conditions that are likely to threaten the 30-day-old individuals occurred more frequently in the lower freshwater parts of the GGD system between the years 2005 and 2018. In the context of climate change, a general increase in temperature is predicted, as well as more frequent and severe hypoxic events, therefore we suggest that local Alosa alosa population recruitment could encounter critical oxy-thermic conditions more frequently in the future if no adaptive management of water resources occurs.     

Detection of refractive photokeratectomy traces during eye banking: impossible with organ culture but possible with an active storage machine: case report

Cell and Tissue Banking - The detection of corneas operated on for refractive surgery [LASIK or photorefractive keratectomy (PRK)] will become a major concern for eye banks in the coming years...