Spatial Analysis of Production by Macrophytes,Phytoplankton and Epiphyton in a Large River System under Different Water-Level Conditions

Relative contributions by macrophytes, epiphyton and phytoplankton to total primary production was estimated in a large (∼300 km²) widening of the St. Lawrence River (Canada), over a 2-year period with contrasting flows and water levels. Spatially-explicit estimates of whole-system production were obtained by combining field measurements with remotely sensed data and empirical models using GIS. Primary production and relative contributions of each producer type differed markedly between open-water and wetland habitats. Spatial differences within each habitat arose from interactions between physical factors including light, water depth, water transit times and wind stress. At the whole-system level, annual primary production represented 105 gC m⁻² y⁻¹, divided roughly equally among phytoplankton (34%), submerged macrophytes (27%), emergent macrophytes (23%) and epiphyton (16%). A 10% decrease in annual flows and 1-m decline in water levels between 2000 and 2001 resulted in a 50% loss of marsh habitat, a 60% increase in phytoplankton production in the open-water zone, and in the appearance of conspicuous filamentous algal mats. Low water levels induced substantial shifts in the spatial configuration and relative importance of primary producers although total river primary production remained stable between years.     

A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm

Background  

Intrabodies are defined as antibody molecules which are ectopically expressed inside the cell. Such intrabodies can be used to visualize or inhibit the targeted antigen in living cells. However, most antibody fragments cannot be used as intrabodies because they do not fold under the reducing conditions of the cell cytosol and nucleus.     

Mitoproteome plasticity of rat brown adipocytes in response to cold acclimation

Cold acclimation induces an adaptative increase in respiration in brown adipose tissue (BAT). A comparative analysis by two-dimensional differential in-gel electrophoresis of mitochondrial protein patterns found in rat control and cold-acclimated BAT was performed. A total of 58 proteins exhibiting significant differences in their abundance was unambiguously identified. Proteins implicated in the major catabolic pathways were up-regulated as were ATP synthase and mitofilin. Moreover, these results support the fact that adipocytes can balance their ATP synthesis and their heat production linked to UCP1-sustained uncoupling.     

Life history traits and dispersal shape neutral genetic diversity in metapopulations

Journal of Mathematical Biology - In insect respiration, oxygen from the air diffuses through a branching system of air-filled tubes to the cells of the body and carbon dioxide produced in cellular...     

Aspergillus tubingensis Endocarditis: A Case Report and Review of the Literature

Mycopathologia - Aspergillus endocarditis is a rare infection that may affect immunocompetent patients following heart valve replacement or heart surgery. We report the case of a 39 year...     

Operationalising emission and toxicity modelling of pesticides in LCA: the OLCA-Pest project contribution

The International Journal of Life Cycle Assessment - Current field emission modelling and toxicity characterisation of pesticides suffer from several shortcomings like mismatches between LCI...     

Induction of Photosynthetic Carbon Fixation in Anoxia Relies on Hydrogenase Activity and Proton-Gradient Regulation-Like1-Mediated Cyclic Electron Flow in Chlamydomonas reinhardtii

The model green microalga Chlamydomonas reinhardtii is frequently subject to periods of dark and anoxia in its natural environment. Here, by resorting to mutants defective in the maturation of the chloroplastic oxygen-sensitive hydrogenases or in Proton-Gradient Regulation-Like1 (PGRL1)-dependent cyclic electron flow around photosystem I (PSI-CEF), we demonstrate the sequential contribution of these alternative electron flows (AEFs) in the reactivation of photosynthetic carbon fixation during a shift from dark anoxia to light. At light onset, hydrogenase activity sustains a linear electron flow from photosystem II, which is followed by a transient PSI-CEF in the wild type. By promoting ATP synthesis without net generation of photosynthetic reductants, the two AEF are critical for restoration of the capacity for carbon dioxide fixation in the light. Our data also suggest that the decrease in hydrogen evolution with time of illumination might be due to competition for reduced ferredoxins between ferredoxin-NADP⁺ oxidoreductase and hydrogenases, rather than due to the sensitivity of hydrogenase activity to oxygen. Finally, the absence of the two alternative pathways in a double mutant pgrl1 hydrogenase maturation factor G-2 is detrimental for photosynthesis and growth and cannot be compensated by any other AEF or anoxic metabolic responses. This highlights the role of hydrogenase activity and PSI-CEF in the ecological success of microalgae in low-oxygen environments.Unicellular photosynthetic organisms such as the green alga Chlamydomonas reinhardtii frequently experience anoxic conditions in their natural habitat, especially during the night when the microbial community consumes the available oxygen. Under anoxia, lack of ATP synthesis by F₁F_O ATP synthase (EC 3.6.3.14) due to the absence of mitochondrial respiration is compensated by the activity of various plant- and bacterial-type fermentative enzymes that drive a sustained glycolytic activity (Mus et al., 2007; Terashima et al., 2010; Grossman et al., 2011; Yang et al., 2014). In C. reinhardtii, upstream glycolytic enzymes, including the reversible glyceraldehyde 3-P dehydrogenase, are located in the chloroplast (Johnson and Alric, 2012). This last enzyme is shared by the glycolysis (oxidative activity) and the Calvin-Benson-Bassham (CBB) cycle (reductive activity; Johnson and Alric, 2013). In dark anoxic conditions, the CBB cycle is inactive, thus avoiding wasteful using up of available ATP and depletion of the required intermediates for glycolysis. On the other side, ability of microalgae to perform photosynthetic carbon fixation when transferred from dark to light in the absence of oxygen might also be critical for adaptation to their environment. In such conditions, not only the linear electron flow (LEF) to Rubisco, but also alternative electron flow (AEF) toward oxygen (chlororespiration, Mehler reaction, and mitochondrial respiration; for review, see Miyake, 2010; Peltier et al., 2010; Cardol et al., 2011) is impaired. Thus, cells need to circumvent a paradoxical situation: the activity of the CBB cycle requires the restoration of the cellular ATP, but the chloroplastic F₁F_O ATP synthase activity is compromised by the impairment of most of the photosynthetic electron flows that usually generate the proton motive force in oxic conditions. Other AEFs, specific to anoxic conditions, should therefore be involved to promote ATP synthesis without net synthesis of NADPH and explain the light-induced restoration of CBB cycle activity.Among enzymes expressed in anoxia, the oxygen-sensitive hydrogenases (HYDA1 and HYDA2 in C. reinhardtii) catalyze the reversible reduction of protons into molecular hydrogen from the oxidation of reduced ferredoxins (FDXs; Florin et al., 2001). Although hydrogen metabolism in microalgae has been largely studied in the last 15 years in perspective of promising future renewable energy carriers (Melis et al., 2000; Kruse et al., 2005; Ghirardi et al., 2009), the physiological role of such an oxygen-sensitive enzyme linked to the photosynthetic pathway has been poorly considered. The 40-year-old proposal that H₂ evolution by hydrogenase is involved in induction of photosynthetic electron transfer after anoxic incubation (Kessler, 1973; Schreiber and Vidaver, 1974) has been only recently demonstrated in C. reinhardtii. Gas exchange measurements showed that H₂ evolution occurs prior to CO₂ fixation upon illumination (Cournac et al., 2002). At light onset after a prolonged period in dark anoxic conditions, the photosynthetic electron flow is mainly a LEF toward hydrogenase (Godaux et al., 2013), and lack of hydrogenase activity in hydrogenase maturation factor EF (hydEF) mutant strain deficient in hydrogenases maturation (Posewitz et al., 2004) induces a lag in induction of PSII activity (Ghysels et al., 2013). In cyanobacteria, the bidirectional Ni-Fe hydrogenase might also work as an electron valve for disposal of electrons generated at the onset of illumination of cells (Cournac et al., 2004) or when excess electrons are generated during photosynthesis, preventing the slowing of the electron transport chain under stress conditions (Appel et al., 2000; Carrieri et al., 2011). The bidirectional Ni-Fe hydrogenase could also dispose of excess of reducing equivalents during fermentation in dark anaerobic conditions, helping to generate ATP and maintaining homeostasis (Barz et al., 2010). A similar role for hydrogenase in setting the redox poise in the chloroplast of C. reinhardtii in anoxia has been recently uncovered (Clowez et al., 2015).Still, the physiological and evolutionary advantages of hydrogenase activity have not been demonstrated so far, and the mechanism responsible for the cessation of hydrogen evolution remains unclear. In this respect, at least three hypotheses have been formulated: (1) the inhibition of hydrogenase by O₂ produced by water photolysis (Ghirardi et al., 1997; Cohen et al., 2005), (2) the competition between ferredoxin-NADP⁺ oxidoreductase (FNR) and hydrogenase activity for reduced FDX (Yacoby et al., 2011), and (3) the inhibition of electron supply to hydrogenases by the proton gradient generated by another AEF, the cyclic electron flow around PSI (PSI-CEF; Tolleter et al., 2011). First described by Arnon (1955), PSI-CEF consists in a reinjection of electrons from reduced FDX or NADPH pool in the plastoquinone (PQ) pool. By generating an additional transthylakoidal proton gradient without producing reducing power, this AEF thus contributes to adjust the ATP/NADPH ratio for carbon fixation in various energetic unfavorable conditions including anoxia (Tolleter et al., 2011; Alric, 2014), high light (Tolleter et al., 2011; Johnson et al., 2014), or low CO₂ (Lucker and Kramer, 2013). In C. reinhardtii, two pathways have been suggested to be involved in PSI-CEF: (1) a type II NAD(P)H dehydrogenase (NDA2; Jans et al., 2008) driving the electrons from NAD(P)H to the PQ pool and (2) a pathway involving Proton Gradient Regulation (PGR) proteins where electrons from reduced FDXs return to the PQ pool or cytochrome b₆f. Not fully understood, this latter pathway comprises at least Proton Gradient Regulation5 (PGR5) and Proton-Gradient Regulation-Like1 (PGRL1) proteins (Iwai et al., 2010; Tolleter et al., 2011; Johnson et al., 2014) and is the major route for PSI-CEF in C. reinhardtii cells placed in anoxia (Alric, 2014).In this work, we took advantage of specific C. reinhardtii mutants defective in hydrogenase activity and PSI-CEF to study photosynthetic electron transfer after a period of dark anoxic conditions. Based on biophysical and physiological complementary studies, we demonstrate that at least hydrogenase activity or PSI-CEF is compulsory for the activity of the CBB cycle and for the survival of the cells submitted to anoxic conditions in their natural habitat.     

Space exploration by dendritic cells requires maintenance of myosin II activity by IP3 receptor 1

Dendritic cells (DCs) patrol the interstitial space of peripheral tissues. The mechanisms that regulate their migration in such constrained environment remain unknown. We here investigated the role of calcium in immature DCs migrating in confinement. We found that they displayed calcium oscillations that were independent of extracellular calcium and more frequently observed in DCs undergoing strong speed fluctuations. In these cells, calcium spikes were associated with fast motility phases. IP₃ receptors (IP₃Rs) channels, which allow calcium release from the endoplasmic reticulum, were identified as required for immature DCs to migrate at fast speed. The IP₃R1 isoform was further shown to specifically regulate the locomotion persistence of immature DCs, that is, their capacity to maintain directional migration. This function of IP₃R1 results from its ability to control the phosphorylation levels of myosin II regulatory light chain (MLC) and the back/front polarization of the motor protein. We propose that by upholding myosin II activity, constitutive calcium release from the ER through IP₃R1 maintains DC polarity during migration in confinement, facilitating the exploration of their environment.     

Reference-free detection of isolated SNPs

Detecting single nucleotide polymorphisms (SNPs) between genomes is becoming a routine task with next-generation sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, discoSnp, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, discoSnp ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, discoSnp requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives. An experimental validation was conducted on an arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs that were tested, 96% were successfully genotyped and truly exhibited polymorphism.