Silencing the mob: disrupting quorum sensing as a means to fight plant disease

Bacteria are able to sense their population's density through a cell–cell communication system, termed ‘quorum sensing’ (QS). This system regulates gene expression in response to cell density through the constant production and detection of signalling molecules. These molecules commonly act as auto‐inducers through the up‐regulation of their own synthesis. Many pathogenic bacteria, including those of plants, rely on this communication system for infection of their hosts. The finding that the countering of QS‐disrupting mechanisms exists in many prokaryotic and eukaryotic organisms offers a promising novel method to fight disease. During the last decade, several approaches have been proposed to disrupt QS pathways of phytopathogens, and hence to reduce their virulence. Such studies have had varied success in vivo, but most lend promising support to the idea that QS manipulation could be a potentially effective method to reduce bacterial‐mediated plant disease. This review discusses the various QS‐disrupting mechanisms found in both bacteria and plants, as well as the different approaches applied artificially to interfere with QS pathways and thus protect plant health.     

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0582-8) contains supplementary material, which is available to authorized users.     

A genetically encoded sensor for H2O2 with expanded dynamic range

Hydrogen peroxide is an important second messenger controlling intracellular signaling cascades by selective oxidation of redox active thiolates in proteins. Changes in intracellular [H₂O₂] can be tracked in real time using HyPer, a ratiometric genetically encoded fluorescent probe. Although HyPer is sensitive and selective for H₂O₂ due to the properties of its sensing domain derived from the Escherichia coli OxyR protein, many applications may benefit from an improvement of the indicator’s dynamic range. We here report HyPer-2, a probe that fills this demand. Upon saturating [H₂O₂] exposure, HyPer-2 undergoes an up to sixfold increase of the ratio F500/F420 versus a threefold change in HyPer. HyPer-2 was generated by a single point mutation A406V from HyPer corresponding to A233V in wtOxyR. This mutation was previously shown to destabilize interface between monomers in OxyR dimers. However, in HyPer-2, the A233V mutation stabilizes the dimer and expands the dynamic range of the probe.     

Effects of rehabilitative interventions on pain, function and physical impairments in people with hand osteoarthritis: a systematic review

Introduction

Hand osteoarthritis (OA) is associated with pain, reduced grip strength, loss of range of motion and joint stiffness leading to impaired hand function and difficulty with daily activities. The effectiveness of different rehabilitation interventions on specific treatment goals has not yet been fully explored. The objective of this systematic review is to provide evidence based knowledge on the treatment effects of different rehabilitation interventions for specific treatment goals for hand OA.

Methods

A computerized literature search of Medline, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), ISI Web of Science, the Physiotherapy Evidence Database (PEDro) and SCOPUS was performed. Studies that had an evidence level of 2b or higher and that compared a rehabilitation intervention with a control group and assessed at least one of the following outcome measures - pain, physical hand function or other measures of hand impairment - were included. The eligibility and methodological quality of trials were systematically assessed by two independent reviewers using the PEDro scale. Treatment effects were calculated using standardized mean difference and 95% confidence intervals.

Results

Ten studies, of which six were of higher quality (PEDro score >6), were included. The rehabilitation techniques reviewed included three studies on exercise, two studies each on laser and heat, and one study each on splints, massage and acupuncture. One higher quality trial showed a large positive effect of 12-month use of a night splint on hand pain, function, strength and range of motion. Exercise had no effect on hand pain or function although it may be able to improve hand strength. Low level laser therapy may be useful for improving range of motion. No rehabilitation interventions were found to improve stiffness.

Conclusions

There is emerging high quality evidence to support that rehabilitation interventions can offer significant benefits to individuals with hand OA. A summary of the higher quality evidence is provided to assist with clinical decision making based on current evidence. Further high-quality research is needed concerning the effects of rehabilitation interventions on specific treatment goals for hand OA.     

Mannan Binding Lectin (MBL) genotypes coding for high MBL serum levels are associated with rheumatoid factor negative rheumatoid arthritis in never smokers

Introduction  

Previous studies have provided inconsistent results on whether variants in the MBL2 gene, coding for the complement-activating mannan-binding lectin (MBL) protein, associate with rheumatoid arthritis (RA). We re-evaluated this in context of the main environmental and genetic risk factors (smoking, HLA-DRB1 'shared epitope' (SE), PTPN22*620W), which predispose to rheumatoid factor (RF) and/or anti-citrullinated-protein antibody (ACPA)-positive RA.     

Nanostructuring of Continuous Gold Film by Laser Radiation Under Surface Plasmon Polariton Resonance Conditions

The physical mechanisms of metallic nanoparticles formation by laser technology were studied. The system air/Au film/glass was irradiated by laser at the conditions of surface plasmon resonance. A surface electromagnetic wave was excited in Kretchmann configuration by the fundamental and second harmonics of the Q-switched YAG/Nd⁺³ laser with pulse power density close to the threshold of melting. Nanostructuring of Au film was observed only for the second harmonic (λ = 0.532 μm) irradiation at the surface plasmon polariton resonance (SPR) conditions. Estimations were done using the interference model of the differently directed plasmon polariton waves excited by a surface electromagnetic wave on the metal surface. It was shown that a regular pattern of locally heated spots can be formed in a metallic film by pulsed laser irradiation. The spatial distribution of this pattern is close to the period of interference. The observed effect of laser nanofragmentation is explained by the self-organization of plasmon polariton subsystem in the process of Au nanoparticles formation at high laser intensity levels. These methods open new possibilities for nanostructured surfaces formation utilizing simple self-organization processes.     

Electronic and molecular structure of M-DNA fragments

To study M-DNA molecular structure (such DNA with transition metal ions placed between the nucleic bases is able to conduct the electric current) and its conductivity mechanisms, we carried out ab initio quantum-mechanical calculations of electronic and spatial structures, thermodynamic characteristics of adenine-thymine (АТ) and guanine-cytosine (GC) base pair complexes with Zn²⁺ and Ni²⁺. To take into account the influence of the alkaline environment, calculations for these complexes were also carried out with hydroxyl and two water molecules. Computations were performed at MP2 level of theory using 6–31+G* basis set. Analogous calculations were carried out for (AC)(TG) stacking dimer of nucleic acid base pairs with two Zn²⁺. The calculation of the interaction energy in complexes has shown the preference of locating the metal ion (instead of the imino proton) between bases in M-DNA. The electronic transition energy calculation has revealed the reduction of the first singlet transition energy in АТ and GC complexes with Ni²⁺ from 4.5 eV to 0.4 - 0.6 eV. Ni²⁺ orbitals take part in the formation of HOMO and LUMO on the complexes investigated. It was shown that charges of metal ions incorporated into complexes with nucleic bases and in dimer decrease significantly.     

Pharmacokinetics, safety and inducible cytokine responses during a phase 1 trial of the oral histone deacetylase inhibitor ITF2357 (givinostat)

ITF2357 (givinostat) is a histone deacetylase inhibitor with antiinflammatory properties at low nanomolar concentrations. We report here a phase I safety and pharmacokinetics trial in healthy males administered 50, 100, 200, 400 or 600 mg orally. After 50 mg, mean maximal plasma concentrations reached 104 nmol/L 2 h after dosing, with a half-life of 6.9 h. After 100 mg, maximal concentration reached 199 nmol/L at 2.1 h with a half-life of 6.0 h. Repeat doses for 7 consecutive days of 50, 100 or 200 mg resulted in nearly the same kinetics. There were no serious adverse effects (AEs) and no organ toxicities. However, there was a dose-dependent but transient fall in platelets. After 7 daily doses of 50 or 100 mg, the mean decrease in platelets of 17 and 25% was not statistically significant and returned to baseline within 14 d. Blood removed from the subjects after oral dosing was cultured ex vivo with endotoxin, and the release of tumor necrosis factor (TNF)-α, interleukin (IL)-1β, IL-6, IL-1Ra, interferon (IFN)-γ and IL-10 was determined. Maximal reduction in IL-1β, TNFα, IL-6 and IFNγ was observed 4 h after dosing but returned to baseline at 12 h. There was no significant reduction in IL-1Ra or IL-10. With daily dosing, the fall in cytokine production in blood cultures observed on day 7 was nearly the same as that of the first day. We conclude that dosing of 50 or 100 mg ITF2357 is safe in healthy humans and transiently but repeatedly reduces the production of proinflammatory cytokines without affecting production of antiinflammatory cytokines.     

Endophytic bacteria enhancing growth and disease resistance of potato (Solanum tuberosum L.)

Priming plants by non-pathogenic bacteria allows the host to save energy and to reduce time needed for development of defense reaction during a pathogen attack. However, information on the role of endophytes in plant defense is limited. Here, the ability of endophytic bacteria to promote growth and resistance of potato plants towards infection by the necrotroph Pectobacterium atrosepticum was studied. A Pseudomonas sp. strain was selected due to antagonism towards bacterial pathogens and a Methylobacterium sp. strain because of efficient plant colonization. The aim of this study was to find if there is any correlation between plant growth promotion and induction of resistance by endophytes of potato, as well as to study the putative mechanisms of endophytes interacting with the plant during resistance induction. Both tested strains promoted growth of potato shoots but only the Pseudomonas sp. increased potato resistance towards the soft rot disease. Induction of disease resistance by the Methylobacterium sp. was inversely proportional to the size of bacterial population used for inoculation. The plant antioxidant system was moderately activated during the induction of resistance by the biocontrol strains. qPCR data on expression of marker genes of induced systemic resistance and acquired systemic resistance in endophyte-infected Arabidopsis plants showed activation of both salicylic acid and jasmonate/ethylene-dependent pathways after challenge inoculation with the pathogen. We suggest that some endophytes have the potential to activate both basal and inducible plant defense systems, whereas the growth promotion by biocontrol strains may not correlate with induction of disease resistance.