Protein ADP-ribosylation in plant–bacterium interactions.

<p><b>(A)</b> Scheme of protein ADP-ribosylation. Covalent attachment of NAD⁺-derived ADP-ribose monomer or polymer to a target protein is MARylation or PARylation. The <i>Pseudomonas syringae</i> effectors HopU1 and HopF2 confer MARylation activity. <i>Arabidopsis</i> AtPARPs bear PARylation activity. Poly(ADP-ribose) chain could be linear or branched. <b>(B)</b> Domain architectures of AtPARPs, AtPARGs, and bacterial effectors HopU1 and HopF2. Abbreviations: ZF, zinc finger domain; WGR, tryptophan-glycine-arginine domain; BRCT, BRCA1 C-terminal domain; HD, helical subdomain; ART, (ADP-ribosyl)transferase domain; SAP, SAF-A/B, Acinus and PIAS domain; NLS, nuclear localization signal; T3S, Type III secretion signal. GGG-X7-QEE is PARG signature. <b>(C)</b> Growth phenotype of <i>Arabidopsis thaliana</i> wild-type Col-0, <i>atparp1parp2</i>, and <i>atparg1</i> mutants. Plants were grown at 23°C, with 45% humidity, 75 μE m^-2s^-1 light, and 12-hour light/12-hour dark photoperiods. The picture was taken at three weeks after germination. <b>(D)</b> A model of protein ADP-ribosylation in plant–bacterium interactions. Perception of MAMPs by PRR complexes activates immune gene transcriptional reprograming via activation of MAP kinase cascades (MPKKKs-MPKKs-MPKs) and leads to various defense responses including callose depositions at the cell wall. Reversible PARylation mediated by PARPs and PARG1 modulates <i>Arabidopsis</i> immune gene transcriptional reprograming. Bacterial effectors HopU1 and HopF2 MARylate GRP7 and MKK4/5, respectively, resulting in reduced PRR transcripts and proteins and MAP kinase inactivation to suppress plant immunity. CW, cell wall; PM, plasma membrane; T3SS, Type III secretion system; P, phosphorylation; TF, transcription factor.</p

Analysis of anti-asthmatic drug patents published in China between 2004 and 2013

<p><b>Introduction</b>: We previously reported that 789 anti-allergic patents were granted in China between 1988 and 2008, but the number of patents seems to have grown much faster in China in recent years. Therefore, it is necessary to analyse the patents for anti-asthmatic products between 2004 and 2013 to give pharmaceutical companies and individuals a better understanding of potential candidates for anti-asthmatic drug development from patents published in China.</p> <p><b>Areas covered</b>: The current report analyses the scientific progress that supports anti-asthmatic drug patent applications and reviews the published patent literature in China from 2004 to 2013.</p> <p><b>Expert opinion</b>: The rapid increase in the number of anti-asthmatic patents in China indicates that more specific discoveries have been made and that more people are aware of the importance of intellectual property protection in China. Holding patents may guarantee protection for an innovative new product.</p

DGC values can be recovered at each of the synapses in the serial chain.

<p>Random synaptic weights of 15 mV and 45 mV were generated between each neuron in a five-neuron serial chain and 100 realizations of this chain were created for analysis. These plots demonstrate that DGC values recovered from entangled pathways (top right, bottom right, and bottom left) along the serial chain mirror those calculated using PGC on the first pathway (top left). This suggests that DGC values represent the direct influence between two neurons similar to the PGC relationship that can be calculated between neurons that are not entangled by mediated influences.</p

Refinement of Connectivity Patterns With Conditional Granger Causality.

<p>Conditional Granger causality was applied to the center block of electrodes (excluding border electrodes) to illustrate the effect of removing mediated influences. For the analysis of each probe the causal effect of each electrode upon each target was conditioned by conditioning out the effects of all other electrodes. The left and right panel shows the results of the conditional analysis for the source and sink measure, respectively. Removing erroneous mediation influences from PGC's causal estimates substantially refined the pattern of causal connections. This is most apparent in the total causality (upper right plots of each panel) where only a few primary electrodes remain, electrodes which may represent the major pathways that were modified by the tetanus.</p

Topology of a Simple Five-Neuron Network Using Pairwise Granger causality.

<p>In panel a) the synaptic weights from N1 to N2 and N4 to N5 have been synaptically coupled. N3 is left uncoupled to demonstrate that a pairwise GC will indicate null connectivity. Equivalent but independent random processes drive each of the five neurons. 100 realizations of this network using Izhikevich's simple neuron model with these weights yields the results shown in panel b) using pairwise Granger causality. These results demonstrate that pairwise Granger causality can not only resolve the difference between null and actual connectivity, but also determine the directionality of those influences.</p

The Relationship Between the Causal Strength From Pairwise Granger causality and Actual Synaptic Weights.

<p>The PGC results from a mono-directional simulation with the weight from neuron 4 to 5 varied from 0–75 mV in increments of 5 mV. Synaptic weight is plotted on the x-axis while the resulting PGC values calculated from the spike timing is plotted on the y-axis. The error bars represent the standard deviation of the results of 100 simulations for each point in the plot. The relationship between synaptic weight and PGC is sigmoid described by Equation 12. Notice that only the region in which the synaptic weights are between 15 mV and 45 mV is linearly related with the magnitude of the causality estimate. Areas in which the synaptic weights are very small or very large will result in a distorted causality value that changes very little.</p

Pairwise causal influences using Granger causality following application of significance thresholds, conditional Granger causality analysis, and removal of mediated influences.

<p>Pairwise causal influences using Granger causality following application of significance thresholds, conditional Granger causality analysis, and removal of mediated influences.</p

Comparison of Causality Values from a Traditional Conditional Granger Causality Analysis and the Computational Alternative Described in the Text.

<p>Direct influences between N2 and N3 were recovered by both methods to allow a comparison of Geweke's subtraction method to CGC. Each point was generated from a Monte Carlo simulation of the serial simulation using randomly generated synaptic weights between 15 mV and 45 mV. This plot suggests that both methods provide results consistent with the linear region expected from the sigmoid plot shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003355#pone-0003355-g004" target="_blank">Figure 4</a>. However, Geweke's subtraction method is computationally simple providing the researcher with a clear advantage in large networks especially under conditions where the structural connectivity is known to be serially arranged.</p

Agronomic Characteristics Related to Grain Yield and Nutrient Use Efficiency for Wheat Production in China

<div><p>In order to make clear the recent status and trend of wheat (<i>Triticum aestivum</i> L.) production in China, datasets from multiple field experiments and published literature were collected to study the agronomic characteristics related to grain yield, fertilizer application and nutrient use efficiency from the year 2000 to 2011. The results showed that the mean grain yield of wheat in 2000–2011 was 5950 kg/ha, while the N, P₂O₅ and K₂O application rates were 172, 102 and 91 kg/ha on average, respectively. The decrease in N and P₂O₅ and increase in K₂O balanced the nutrient supply and was the main reason for yield increase. The partial factor productivity (PFP, kg grain yield produced per unit of N, P₂O₅ or K₂O applied) values of N (PFP-N), P (PFP-P) and K (PFP-K) were in the ranges of 29.5~39.6, 43.4~74.9 and 44.1~76.5 kg/kg, respectively. While PFP-N showed no significant changes from 2000 to 2010, both PFP-P and PFP-K showed an increased trend over this period. The mean agronomic efficiency (AE, kg grain yield increased per unit of N, P₂O₅ or K₂O applied) values of N (AEN), P (AEP) and K (AEK) were 9.4, 10.2 and 6.5 kg/kg, respectively. The AE values demonstrated marked inter-annual fluctuations, with the amplitude of fluctuation for AEN greater than those for AEP and AEK. The mean fertilizer recovery efficiency (RE, the fraction of nutrient uptake in aboveground plant dry matter to the nutrient of fertilizer application) values of N, P and K in the aboveground biomass were 33.1%, 24.3% and 28.4%, respectively. It was also revealed that different wheat ecological regions differ greatly in wheat productivity, fertilizer application and nutrient use efficiency. In summary, it was suggested that best nutrient management practices, i.e. fertilizer recommendation applied based on soil testing or yield response, with strategies to match the nutrient input with realistic yield and demand, or provided with the 4R’s nutrient management (right time, right rate, right site and right fertilizer) should be adopted widely to improve the yield production and nutrient use efficiency.</p></div

Changes of grain yield and fertilizer application for wheat in all treatments within different years (A), and for wheat only in OPT (B) and FP plots (C), respectively, and comparison of grain yield between OPT, FP plots and the yearbook (D) in different years.

<p>Changes of grain yield and fertilizer application for wheat in all treatments within different years (A), and for wheat only in OPT (B) and FP plots (C), respectively, and comparison of grain yield between OPT, FP plots and the yearbook (D) in different years.</p