Comparing the performance of FA, DFA and DMA using different synthetic long-range correlated time series

Notwithstanding the significant efforts to develop estimators of long-range correlations (LRC) and to compare their performance, no clear consensus exists on what is the best method and under which conditions. In addition, synthetic tests suggest that the performance of LRC estimators varies when using different generators of LRC time series. Here, we compare the performances of four estimators [Fluctuation Analysis (FA), Detrended Fluctuation Analysis (DFA), Backward Detrending Moving Average (BDMA), and centred Detrending Moving Average (CDMA)]. We use three different generators [Fractional Gaussian Noises, and two ways of generating Fractional Brownian Motions]. We find that CDMA has the best performance and DFA is only slightly worse in some situations, while FA performs the worst. In addition, CDMA and DFA are less sensitive to the scaling range than FA. Hence, CDMA and DFA remain "The Methods of Choice" in determining the Hurst index of time series.Comment: 6 pages (including 3 figures) + 3 supplementary figure

Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome

Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3′ ends of tRNA ligands. Here we present structures, at 3.6-Å and 3.5-Å resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer

Variations in task constraints shape emergent performance outcomes and complexity levels in balancing

This study investigated the extent to which specific interacting constraints of performance might increase or decrease the emergent complexity in a movement system, and whether this could affect the relationship between observed movement variability and the central nervous system's capacity to adapt to perturbations during balancing. Fifty-two healthy volunteers performed eight trials where different performance constraints were manipulated: task difficulty (three levels) and visual biofeedback conditions (with and without the center of pressure (COP) displacement and a target displayed). Balance performance was assessed using COP-based measures: mean velocity magnitude (MVM) and bivariate variable error (BVE). To assess the complexity of COP, fuzzy entropy (FE) and detrended fluctuation analysis (DFA) were computed. ANOVAs showed that MVM and BVE increased when task difficulty increased. During biofeedback conditions, individuals showed higher MVM but lower BVE at the easiest level of task difficulty. Overall, higher FE and lower DFA values were observed when biofeedback was available. On the other hand, FE reduced and DFA increased as difficulty level increased, in the presence of biofeedback. However, when biofeedback was not available, the opposite trend in FE and DFA values was observed. Regardless of changes to task constraints and the variable investigated, balance performance was positively related to complexity in every condition. Data revealed how specificity of task constraints can result in an increase or decrease in complexity emerging in a neurobiological system during balance performance

Endophytes vs tree pathogens and pests: can they be used as biological control agents to improve tree health?

Like all other plants, trees are vulnerable to attack by a multitude of pests and pathogens. Current control measures for many of these diseases are limited and relatively ineffective. Several methods, including the use of conventional synthetic agro-chemicals, are employed to reduce the impact of pests and diseases. However, because of mounting concerns about adverse effects on the environment and a variety of economic reasons, this limited management of tree diseases by chemical methods is losing ground. The use of biological control, as a more environmentally friendly alternative, is becoming increasingly popular in plant protection. This can include the deployment of soil inoculants and foliar sprays, but the increased knowledge of microbial ecology in the phytosphere, in particular phylloplane microbes and endophytes, has stimulated new thinking for biocontrol approaches. Endophytes are microbes that live within plant tissues. As such, they hold potential as biocontrol agents against plant diseases because they are able to colonize the same ecological niche favoured by many invading pathogens. However, the development and exploitation of endophytes as biocontrol agents will have to overcome numerous challenges. The optimization and improvement of strategies employed in endophyte research can contribute towards discovering effective and competent biocontrol agents. The impact of environment and plant genotype on selecting potentially beneficial and exploitable endophytes for biocontrol is poorly understood. How endophytes synergise or antagonise one another is also an important factor. This review focusses on recent research addressing the biocontrol of plant diseases and pests using endophytic fungi and bacteria, alongside the challenges and limitations encountered and how these can be overcome. We frame this review in the context of tree pests and diseases, since trees are arguably the most difficult plant species to study, work on and manage, yet they represent one of the most important organisms on Earth

Production of a potential liquid plant bio-stimulant by immobilized Piriformospora indica in repeated-batch fermentation process

Piriformospora indica, a mycorrhizal-like fungus able to establish associations with roots of a wide range of plants, supporting plant nutrition and increasing plant resistance and tolerance to stress, was shown to solubilise phosphate applied in the form of animal bone char (HABO) in fermentation systems. The process of P solubilisation was caused most likely by proton extrusion and medium pH lowering. The fungal mycelium was successfully immobilized/retained in a polyurethane foam carrier. Further employment of the immobilized mycelium in repeated-batch fermentation process resulted in at least 5 cycles of P solubilization. The concentration of soluble P increased during the experiment with 1.0 and 3.0 g HABO l−1 and at the end of the 5th batch cycle reached 40.8 and 120 mg l−1, respectively. The resulting final liquid product, without or with solubilized phosphate, was found to significantly increase plant growth and P plant uptake. It can be used as a biostimulant containing microbial plant growth-promoting substances and soluble P derived from renewable sources (HABO) thus supporting the development of sustainable agro-ecosystems.This work was supported by Project CTM2014-53186-R, Ministerio de Economia y Competitividad-ES/EC FEDER Fund and the sabbatical Grant PRX16/00277 to NV

Endophytes vs tree pathogens and pests: can they be used as biological control agents to improve tree health?

Like all other plants, trees are vulnerable to attack by a multitude of pests and pathogens. Current control measures for many of these diseases are limited and relatively ineffective. Several methods, including the use of conventional synthetic agro-chemicals, are employed to reduce the impact of pests and diseases. However, because of mounting concerns about adverse effects on the environment and a variety of economic reasons, this limited management of tree diseases by chemical methods is losing ground. The use of biological control, as a more environmentally friendly alternative, is becoming increasingly popular in plant protection. This can include the deployment of soil inoculants and foliar sprays, but the increased knowledge of microbial ecology in the phytosphere, in particular phylloplane microbes and endophytes, has stimulated new thinking for biocontrol approaches. Endophytes are microbes that live within plant tissues. As such, they hold potential as biocontrol agents against plant diseases because they are able to colonize the same ecological niche favoured by many invading pathogens. However, the development and exploitation of endophytes as biocontrol agents will have to overcome numerous challenges. The optimization and improvement of strategies employed in endophyte research can contribute towards discovering effective and competent biocontrol agents. The impact of environment and plant genotype on selecting potentially beneficial and exploitable endophytes for biocontrol is poorly understood. How endophytes synergise or antagonise one another is also an important factor. This review focusses on recent research addressing the biocontrol of plant diseases and pests using endophytic fungi and bacteria, alongside the challenges and limitations encountered and how these can be overcome. We frame this review in the context of tree pests and diseases, since trees are arguably the most difficult plant species to study, work on and manage, yet they represent one of the most important organisms on Earth

Microalgae cultivation in wastewater: nutrient removal from anaerobic membrane bioreactor effluent

This study investigated the removal of nitrogen and phosphorus from the effluent of a submerged anaerobic membrane bioreactor (SAnMBR) by means of a lab-scale photobioreactor in which algae biomass was cultured in a semi-continuous mode for a period of 42 days. Solids retention time was 2 days and a stable pH value in the system was maintained by adding CO2. Nitrogen and phosphorus concentrations in the SAnMBR effluent fluctuated according to the operating performance of the bioreactor and the properties of its actual wastewater load. Despite these variations, the anaerobic effluent proved to be a suitable growth medium for microalgae (mean biomass productivity was 234 mgl(-1) d(-1)), achieving a nutrient removal efficiency of 67.2% for ammonium (NH4+-N) and 97.8% for phosphate (PO4-3-P). When conditions were optimum, excellent water quality with very low ammonium and phosphate concentrations was obtained.This research project has been supported by the Spanish Research Foundation (CICYT, projects CTM2011-28595-C02-01 and CTM2011-28595-C02-02), whose support is gratefully acknowledged.Ruiz Martínez, A.; Martin Garcia, N.; Romero Gil, I.; Seco, A.; Ferrer, J. (2012). Microalgae cultivation in wastewater: nutrient removal from anaerobic membrane bioreactor effluent. Bioresource Technology. 126:247-253. https://doi.org/10.1016/j.biortech.2012.09.022S24725312

A-Site Residues Move Independently from P-Site Residues in all-Atom Molecular Dynamics Simulations of the 70S Bacterial Ribosome

The ribosome is a large macromolecular machine, and correlated motion between residues is necessary for coordinating function across multiple protein and RNA chains. We ran two all-atom, explicit solvent molecular dynamics simulations of the bacterial ribosome and calculated correlated motion between residue pairs by using mutual information. Because of the short timescales of our simulation (ns), we expect that dynamics are largely local fluctuations around the crystal structure. We hypothesize that residues that show coupled dynamics are functionally related, even on longer timescales. We validate our model by showing that crystallographic B-factors correlate well with the entropy calculated as part of our mutual information calculations. We reveal that A-site residues move relatively independently from P-site residues, effectively insulating A-site functions from P-site functions during translation