Effects of cyanide and dissolved oxygen concentration on biological Au recovery

The number of discarded electric devices containing traces of Au is currently increasing. It is desirable to recover this Au because of its valuable physicochemical properties. Au is usually dissolved with relatively high concentrations of cyanide, which is associated with environmental risk. Chromobacterium violaceum is able to produce and detoxify small amounts of cyanide, and may thus be able to recover Au from discarded electric devices. This study investigated the effects of cyanide and dissolved oxygen concentration on biological Au recovery. Cyanide production by C. violaceum was sufficient to dissolve Au, while maintaining a high cyanide concentration did not enhance Au dissolution. Increased oxygen concentration enhanced Au dissolution from 0.04 to 0.16 mmol/l within the test period of 70 h. Electrochemical measurement clarified this phenomenon; the rest potential of Au in the cyanide solution produced by C. violaceum increased from -400 to -200 mV, while in the sterile cyanide solution, it was constant in cyanide concentrations ranging from 0 to 1.5 mmol/l and increased in dissolved oxygen concentrations ranging from 0 to 0.25 mmol/l. Therefore, it was clarified that dissolved oxygen concentration is the main factor affecting the efficiency of cyanide leaching of gold by using bacteria.     

N-terminal motifs in some plant disease resistance proteins function in membrane attachment and contribute to disease resistance

To investigate the role of N-terminal domains of plant disease resistance proteins in membrane targeting, the N termini of a number of Arabidopsis and flax disease resistance proteins were fused to green fluorescent protein (GFP) and the fusion proteins localized in planta using confocal microscopy. The N termini of the Arabidopsis RPP1-WsB and RPS5 resistance proteins and the PBS1 protein, which is required for RPS5 resistance, targeted GFP to the plasma membrane, and mutation of predicted myristoylation and potential palmitoylation sites resulted in a shift to nucleocytosolic localization. The N-terminal domain of the membrane-attached Arabidopsis RPS2 resistance protein was targeted incompletely to the plasma membrane. In contrast, the N-terminal domains of the Arabidopsis RPP1-WsA and flax L6 and M resistance proteins, which carry predicted signal anchors, were targeted to the endomembrane system, RPP1-WsA to the endoplasmic reticulum and the Golgi apparatus, L6 to the Golgi apparatus, and M to the tonoplast. Full-length L6 was also targeted to the Golgi apparatus. Site-directed mutagenesis of six nonconserved amino acid residues in the signal anchor domains of L6 and M was used to change the localization of the L6 N-terminal fusion protein to that of M and vice versa, showing that these residues control the targeting specificity of the signal anchor. Replacement of the signal anchor domain of L6 by that of M did not affect L6 protein accumulation or resistance against flax rust expressing AvrL567 but removal of the signal anchor domain reduced L6 protein accumulation and L6 resistance, suggesting that membrane attachment is required to stabilize the L6 protein.     

Functional analysis of an indole-diterpene gene cluster for lolitrem B biosynthesis in the grass endosymbiont Epichloë festucae

Epichloë festucae Fl1 in association with Lolium perenne synthesizes a diverse range of indole-diterpene bioprotective metabolites, including lolitrem B, a potent tremorgen. The ltm genes responsible for the synthesis of these metabolites are organized in three clusters at a single sub-telomeric locus in the genome of E. festucae. Here we resolve the genetic basis for the remarkable indole-diterpene diversity observed in planta by analyzing products that accumulate in associations containing ltm deletion mutants of E. festucae and in cells of Penicillium paxilli containing copies of these genes under the control of a P. paxilli biosynthetic gene promoter. We propose a biosynthetic scheme to account for this metabolic diversity.     

Self-assembly of amylose-grafted carboxymethyl cellulose

In this study, we performed the self-assembly of the amylose-grafted carboxymethyl cellulose sodium salt (NaCMC) for the formation of nanofiber films under aqueous conditions. The introduction of amylose graft chains was conducted by the chemoenzymatic approach including phosphorylase-catalyzed enzymatic polymerization. The product had the rigid NaCMC main chain, which further assembled leading to nanofibers by the formation of double helix between the long amylose graft chains in the intermolecular NaCMC chains of the products. The lengths of the fibers were depended on degrees of polymerization of amylose chains. The nanofiber films were constructed by drying the alkaline solutions of the amylose-grafted NaCMC. The lengths of the nanofibers strongly affected their arrangements in the films. The nanofibers were merged further by washing out alkali to produce the robust nanofiber films.     

Establishment of a set of inbred strains of the pine wood nematode, Bursaphelenchus xylophilus (Aphelenchida: Aphelenchoididae), and evidence of their varying levels of virulence

Pine wilt disease (PWD) caused by the pine wood nematode, Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle, has become a worldwide problem. The pathogenic mechanism of PWD continues to remain controversial, which in part may be attributed to the lack of universal materials of B. xylophilus with a high genetic purity. The intrinsic high genetic diversity in B. xylophilus isolates/populations must be a fatal obstacle for performing forward genetics and other molecular approaches to controlling them. We conducted a series of successive full-sib mating of conventional isolates of B. xylophilus to establish a set of inbred strains. Using DNA markers, we also determined their genetic diversity and biological characteristics, such as virulence and reproductive ability. Consequently, the newly established strains yielded a higher genetic purity than the conventional isolates and showed varying virulence despite sharing a common ancestor. The significance of this study lies not only in establishing a set of inbred strains of B. xylophilus with the certification of their purity but also in demonstrating that avirulent strain(s) with a genotype similar to the virulent strains can be obtained by simple successive full-sib mating. This technique is one of the most powerful tools for elucidating the pathogenic mechanism(s) of PWD.     

System dynamics to model the unintended consequences of denying payment for venous thromboembolism after total knee arthroplasty

Background

The Hospital Acquired Condition Strategy (HACS) denies payment for venous thromboembolism (VTE) after total knee arthroplasty (TKA). The intention is to reduce complications and associated costs, while improving the quality of care by mandating VTE prophylaxis. We applied a system dynamics model to estimate the impact of HACS on VTE rates, and potential unintended consequences such as increased rates of bleeding and infection and decreased access for patients who might benefit from TKA.

Methods and Findings

The system dynamics model uses a series of patient stocks including the number needing TKA, deemed ineligible, receiving TKA, and harmed due to surgical complication. The flow of patients between stocks is determined by a series of causal elements such as rates of exclusion, surgery and complications. The number of patients harmed due to VTE, bleeding or exclusion were modeled by year by comparing patient stocks that results in scenarios with and without HACS. The percentage of TKA patients experiencing VTE decreased approximately 3-fold with HACS. This decrease in VTE was offset by an increased rate of bleeding and infection. Moreover, results from the model suggest HACS could exclude 1.5% or half a million patients who might benefit from knee replacement through 2020.

Conclusion

System dynamics modeling indicates HACS will have the intended consequence of reducing VTE rates. However, an unintended consequence of the policy might be increased potential harm resulting from over administration of prophylaxis, as well as exclusion of a large population of patients who might benefit from TKA.     

Fungal endophytes of grasses

Epichloae endophytes form mutualistic symbiotic associations with temperate grasses and confer on the host a number of bioprotective benefits through production of fungal secondary metabolites and changed host metabolism. Maintenance of this mutualistic interaction requires that growth of the endophyte within the host is restricted. Recent work has shown that epichloae endophytes grow in the leaves by intercalary division and extension rather than tip growth. This novel pattern of growth enables the fungus to synchronise its growth with that of the host. Reactive oxygen species signalling is required to maintain this pattern of growth. Disruption of components of the NADPH oxidase complex or a MAP kinase, result in a switch from restricted to proliferative growth and a breakdown in the symbiosis. RNAseq analysis of mutant and wild-type associations identifies key fungal and plant genes that define the symbiotic state. Endophyte genes for secondary metabolite biosynthesis are only expressed in the plant and under conditions of restricted growth.     

Accelerated polymer-polymer click conjugation by freeze-thaw treatment

Herein, we report a unique technique to accelerate polymer-SNA conjugation based on copper-free click chemistry: gradual freeze-thawing of the reaction solution substantially increases the conjugation rate possibly because of the reactant concentration at the microenvironment scale. This technique was applied to the conjugation between a small interfering RNA (siRNA) and PEG in an aqueous buffer at/below room temperature.     

FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

Single amino acid variants (SAVs) are the most abundant form of known genetic variations associated with human disease. Successful prediction of the functional impact of SAVs from sequences can thus lead to an improved understanding of the underlying mechanisms of why a SAV may be associated with certain disease. In this work, we constructed a high-quality structural dataset that contained 679 high-quality protein structures with 2,048 SAVs by collecting the human genetic variant data from multiple resources and dividing them into two categories, i.e., disease-associated and neutral variants. We built a two-stage random forest (RF) model, termed as FunSAV, to predict the functional effect of SAVs by combining sequence, structure and residue-contact network features with other additional features that were not explored in previous studies. Importantly, a two-step feature selection procedure was proposed to select the most important and informative features that contribute to the prediction of disease association of SAVs. In cross-validation experiments on the benchmark dataset, FunSAV achieved a good prediction performance with the area under the curve (AUC) of 0.882, which is competitive with and in some cases better than other existing tools including SIFT, SNAP, Polyphen2, PANTHER, nsSNPAnalyzer and PhD-SNP. The sourcecodes of FunSAV and the datasets can be downloaded at http://sunflower.kuicr.kyoto-u.ac.jp/sjn/FunSAV.