Effects of Submerged Vegetation on Water Clarity Across Climates

A positive feedback between submerged vegetation and water clarity forms the backbone of the alternative state theory in shallow lakes. The water clearing effect of aquatic vegetation may be caused by different physical, chemical, and biological mechanisms and has been studied mainly in temperate lakes. Recent work suggests differences in biotic interactions between (sub)tropical and cooler lakes might result in a less pronounced clearing effect in the (sub)tropics. To assess whether the effect of submerged vegetation changes with climate, we sampled 83 lakes over a gradient ranging from the tundra to the tropics in South America. Judged from a comparison of water clarity inside and outside vegetation beds, the vegetation appeared to have a similar positive effect on the water clarity across all climatic regions studied. However, the local clearing effect of vegetation decreased steeply with the contribution of humic substances to the underwater light attenuation. Looking at turbidity on a whole-lake scale, results were more difficult to interpret. Although lakes with abundant vegetation (>30%) were generally clear, sparsely vegetated lakes differed widely in clarity. Overall, the effect of vegetation on water clarity in our lakes appears to be smaller than that found in various Northern hemisphere studies. This might be explained by differences in fish communities and their relation to vegetation. For instance, unlike in Northern hemisphere studies, we find no clear relation between vegetation coverage and fish abundance or their diet preference. High densities of omnivorous fish and coinciding low grazing pressures on phytoplankton in the (sub)tropics may, furthermore, weaken the effect of vegetation on water clarity.     

Metabolic Engineering with power-law and linear-logarithmic systems

Metabolic Engineering aims to improve the performance of biotechnological processes through rational manipulation rather than random mutagenesis of the organisms involved. Such a strategy can only succeed when a mathematical model of the target process is available. Simplifying assumptions are often needed to cope with the complexity of such models in an efficient way, and the choice of such assumptions often leads to models that fall within a certain structural template or formalism. The most popular formalisms can be grouped in two categories: power-law and linear-logarithmic. As optimization and analysis of a model strongly depends on its structure, most methods in Metabolic Engineering have been defined within a given formalism and never used in any other.In this work, the four most commonly used formalisms (two power-law and two linear-logarithmic) are placed in a common framework defined within Biochemical Systems Theory. This framework defines every model as matrix equations in terms of the same parameters, enabling the formulation of a common steady state analysis and providing means for translating models and methods from one formalism to another. Several Metabolic Engineering methods are analysed here and shown to be variants of a single equation. Particularly, two problem solving philosophies are compared: the application of the design equation and the solution of constrained optimization problems. Generalizing the design equation to all the formalisms shows it to be interchangeable with the direct solution of the rate law in matrix form. Furthermore, optimization approaches are concluded to be preferable since they speed the exploration of the feasible space, implement a better specification of the problem and exclude unrealistic results.Beyond consolidating existing knowledge and enabling comparison, the systematic approach adopted here can fill the gaps between the different methods and combine their strengths.     

Dengue Virus Capsid Protein Usurps Lipid Droplets for Viral Particle Formation

Dengue virus is responsible for the highest rates of disease and mortality among the members of the Flavivirus genus. Dengue epidemics are still occurring around the world, indicating an urgent need of prophylactic vaccines and antivirals. In recent years, a great deal has been learned about the mechanisms of dengue virus genome amplification. However, little is known about the process by which the capsid protein recruits the viral genome during encapsidation. Here, we found that the mature capsid protein in the cytoplasm of dengue virus infected cells accumulates on the surface of ER-derived organelles named lipid droplets. Mutagenesis analysis using infectious dengue virus clones has identified specific hydrophobic amino acids, located in the center of the capsid protein, as key elements for lipid droplet association. Substitutions of amino acid L50 or L54 in the capsid protein disrupted lipid droplet targeting and impaired viral particle formation. We also report that dengue virus infection increases the number of lipid droplets per cell, suggesting a link between lipid droplet metabolism and viral replication. In this regard, we found that pharmacological manipulation of the amount of lipid droplets in the cell can be a means to control dengue virus replication. In addition, we developed a novel genetic system to dissociate cis-acting RNA replication elements from the capsid coding sequence. Using this system, we found that mislocalization of a mutated capsid protein decreased viral RNA amplification. We propose that lipid droplets play multiple roles during the viral life cycle; they could sequester the viral capsid protein early during infection and provide a scaffold for genome encapsidation.     

Testing the metabolic theory of ecology with marine bacteria: different temperature sensitivity of major phylogenetic groups during the spring phytoplankton bloom

Although temperature is a key driver of bacterioplankton metabolism, the effect of ocean warming on different bacterial phylogenetic groups remains unclear. Here, we conducted monthly short‐term incubations with natural coastal bacterial communities over an annual cycle to test the effect of experimental temperature on the growth rates and carrying capacities of four phylogenetic groups: SAR11, Rhodobacteraceae, Gammaproteobacteria and Bacteroidetes. SAR11 was the most abundant group year‐round as analysed by CARD‐FISH, with maximum abundances in summer, while the other taxa peaked in spring. All groups, including SAR11, showed high temperature‐sensitivity of growth rates and/or carrying capacities in spring, under phytoplankton bloom or post‐bloom conditions. In that season, Rhodobacteraceae showed the strongest temperature response in growth rates, estimated here as activation energy (E, 1.43 eV), suggesting an advantage to outcompete other groups under warmer conditions. In summer E values were in general lower than 0.65 eV, the value predicted by the Metabolic Theory of Ecology (MTE). Contrary to MTE predictions, carrying capacity tended to increase with warming for all bacterial groups. Our analysis confirms that resource availability is key when addressing the temperature response of heterotrophic bacterioplankton. We further show that even under nutrient‐sufficient conditions, warming differentially affected distinct bacterioplankton taxa.     

Unraveling the decolourizing ability of yeast isolates from dye-polluted and virgin environments: an ecological and taxonomical overview

Microcosm assays with dye-amended culture media under a shot-feeding strategy allowed us to obtain 100 yeast isolates from the wastewater outfall channel of a dyeing textile factory in Tucumán (Argentina). Meanwhile, 63 yeast isolates were obtained from Phoebe porphyria (Laurel del monte) samples collected from Las Yungas rainforest (Tucumán), via a classical isolation scheme. Isolated yeasts, both from dye-polluted and virgin environments, were compared for their textile dye decolourization ability when cultured on solid and liquid media. Nine isolates from wastewater and 17 from Las Yungas showed the highest decolourization potential on agar plates containing six different reactive dyes, either alone or as a mixture. Five yeasts from each environment were further selected on the basis of their high dye removal rate in Vilmafix^® Red 7B-HE- or Vilmafix^® Blue RR-BB-amended liquid cultures. Yeasts from wastewater showed slightly higher decolourization percentages after 36 h of culture than yeasts from Las Yungas (98?C100% vs. 91?C95%, respectively). However, isolates from Las Yungas exhibited higher specific decolourization rates than isolates from effluents (1.8?C3.0 vs. 0.9?C1.3 mg g^?1h^?1, respectively). All selected isolates were first grouped according to microsatellite-PCR analysis and representative isolates from each group were subsequently identified based on the 26S rRNA gene sequence analysis. Yeasts from wastewater were identified as the ascomycetous Pichia kudriavzevii (100%) and closely related to Candida sorbophila (99.8%), whilst yeasts from Las Yungas were identified as the basidiomycetous Trichosporon akiyoshidainum and Trichosporon multisporum. It is suggested that findings concerning yeast selection during screening programs for dye-decolourizing yeasts may be explained in the light of the copiotroph-oligotroph microorganisms rationale.     

The reaction of H(2)S with oxidized thiols: generation of persulfides and implications to H(2)S biology

Hydrogen sulfide is an endogenously generated molecule with many reported physiological functions. Although several biological targets have been proposed, the biochemical mechanisms by which it elicits activity are not established. Thus, in an effort to begin to delineate the fundamental biological chemistry of H₂S, we have examined the reaction of H₂S with oxidized thiols and thiol proteins in order to determine whether persulfide formation occurs, is stable and how this may affect protein function. We have found that persulfides are easily generated, relatively stable and can alter enzyme activity. Moreover, we have begun to develop methodology for in situ generation of persulfides to facilitate further study of this potentially important species.     

Bromeliad growth and stoichiometry: responses to atmospheric nutrient supply in fog-dependent ecosystems of the hyper-arid Atacama Desert, Chile

Carbon, nitrogen, and phosphorus (C, N, P) stoichiometry influences the growth of plants and nutrient cycling within ecosystems. Indeed, elemental ratios are used as an index for functional differences between plants and their responses to natural or anthropogenic variations in nutrient supply. We investigated the variation in growth and elemental content of the rootless terrestrial bromeliad Tillandsia landbeckii, which obtains its moisture, and likely its nutrients, from coastal fogs in the Atacama Desert. We assessed (1) how fog nutrient supply influences plant growth and stoichiometry and (2) the response of plant growth and stoichiometry to variations in nutrient supply by using reciprocal transplants. We hypothesized that T. landbeckii should exhibit physiological and biochemical plastic responses commensurate with nutrient supply from atmospheric deposition. In the case of the Atacama Desert, nutrient supply from fog is variable over space and time, which suggests a relatively high variation in the growth and elemental content of atmospheric bromeliads. We found that the nutrient content of T. landbeckii showed high spatio-temporal variability, driven partially by fog nutrient deposition but also by plant growth rates. Reciprocal transplant experiments showed that transplanted individuals converged to similar nutrient content, growth rates, and leaf production of resident plants at each site, reflecting local nutrient availability. Although plant nutrient content did not exactly match the relative supply of N and P, our results suggest that atmospheric nutrient supply is a dominant driver of plant growth and stoichiometry. In fact, our results indicate that N uptake by T. landbeckii plants depends more on N supplied by fog, whereas P uptake is mainly regulated by within-plant nutrient demand for growth. Overall, these findings indicate that variation in fog nutrient supply exerts a strong control over growth and nutrient dynamics of atmospheric plants, which are ubiquitous across fog-dominated ecosystems.     

The F1 motif of dengue virus polymerase NS5 is involved in promoter-dependent RNA synthesis

The mechanism by which viral RNA-dependent RNA polymerases (RdRp) specifically amplify viral genomes is still unclear. In the case of flaviviruses, a model has been proposed that involves the recognition of an RNA element present at the viral 5' untranslated region, stem-loop A (SLA), that serves as a promoter for NS5 polymerase binding and activity. Here, we investigated requirements for specific promoter-dependent RNA synthesis of the dengue virus NS5 protein. Using mutated purified NS5 recombinant proteins and infectious viral RNAs, we analyzed the requirement of specific amino acids of the RdRp domain on polymerase activity and viral replication. A battery of 19 mutants was designed and analyzed. By measuring polymerase activity using nonspecific poly(rC) templates or specific viral RNA molecules, we identified four mutants with impaired polymerase activity. Viral full-length RNAs carrying these mutations were found to be unable to replicate in cell culture. Interestingly, one recombinant NS5 protein carrying the mutations K456A and K457A located in the F1 motif lacked RNA synthesis dependent on the SLA promoter but displayed high activity using a poly(rC) template. Promoter RNA binding of this NS5 mutant was unaffected while de novo RNA synthesis was abolished. Furthermore, the mutant maintained RNA elongation activity, indicating a role of the F1 region in promoter-dependent initiation. In addition, four NS5 mutants were selected to have polymerase activity in the recombinant protein but delayed or impaired virus replication when introduced into an infectious clone, suggesting a role of these amino acids in other functions of NS5. This work provides new molecular insights on the specific RNA synthesis activity of the dengue virus NS5 polymerase.     

Seabird ticks (Ixodes uriae) distribution along the Antarctic Peninsula

The distribution of the tick Ixodes uriae is studied in the South Shetlands and different locations along the Antarctic Peninsula. Ticks were found beneath stones close to penguin rookeries of chinstrap, gentoo and adelie penguin, although no individuals were found parasitized. Our results showed that ticks are not distributed evenly along the Antarctic Peninsula being more common and abundant in the northern part with relative abundances of ticks ranging from 1 to 57 individuals per stone and from 2 to 26% of the stone inspected. Ticks are probably absent in the south.