Multiple quantitative trait loci contribute to resistance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis)

Pseudomonas syringae pv. actinidiae (Psa) biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidia spp.) industry worldwide. The commercially grown diploid (2×) A. chinensis var. chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulating Psa resistance in kiwifruit is not available. Here we report mapping of quantitative trait loci (QTLs) regulating resistance to Psa in a diploid kiwifruit population, derived from a cross between an elite Psa-susceptible 'Hort16A' and a resistant male breeding parent P1. Using high-density genetic maps and intensive phenotyping, we identified a single QTL for Psa resistance on Linkage Group (LG) 27 of 'Hort16A' revealing 16-19% phenotypic variance and candidate alleles for susceptibility and resistance at this loci. In addition, six minor QTLs were identified in P1 on distinct LGs, exerting 4-9% variance. Resistance in the F1 population is improved by additive effects from 'Hort16A' and P1 QTLs providing evidence that divergent genetic pathways interact to combat the virulent Psa strain. Two different bioassays further identified new QTLs for tissue-specific responses to Psa. The genetic marker at LG27 QTL was further verified for association with Psa resistance in diploid Actinidia chinensis populations. Transcriptome analysis of Psa-resistant and susceptible genotypes in field revealed hallmarks of basal defense and provided candidate RNA-biomarkers for screening for Psa resistance in greenhouse conditions.

Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease

The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries--even millennia--ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease.

Energetic valorization of wood waste: estimation of the reduction in CO2 emissions

This paper investigates the potential CO(2) emission reductions related to a partial switch from fossil fuel-based heat and electricity generation to renewable wood waste-based systems in Flanders. The results show that valorization in large-scale CHP (combined heat and power) systems and co-firing in coal plants have the largest CO(2) reduction per TJ wood waste. However, at current co-firing rates of 10%, the CO(2) reduction per GWh of electricity that can be achieved by co-firing in coal plants is five times lower than the CO(2) reduction per GWh of large-scale CHP. Moreover, analysis of the effect of government support for co-firing of wood waste in coal-fired power plants on the marginal costs of electricity generation plants reveals that the effect of the European Emission Trading Scheme (EU ETS) is effectively counterbalanced. This is due to the fact that biomass integrated gasification combined cycles (BIGCC) are not yet commercially available. An increase of the fraction of coal-based electricity in the total electricity generation from 8 to 10% at the expense of the fraction of gas-based electricity due to the government support for co-firing wood waste, would compensate entirely for the CO(2) reduction by substitution of coal by wood waste. This clearly illustrates the possibility of a 'rebound' effect on the CO(2) reduction due to government support for co-combustion of wood waste in an electricity generation system with large installed capacity of coal- and gas-based power plants, such as the Belgian one.

Scalar decay in a three-dimensional chaotic flow

The decay of a passive scalar in a three-dimensional chaotic flow is studied using high-resolution numerical simulations. The (volume-preserving) flow considered is a three-dimensional extension of the randomized alternating sine flow employed extensively in studies of mixing in two dimensions. It is used to show that theoretical predictions for two-dimensional flows with small diffusivity carry over to three dimensions even though the stretching properties differ significantly. The variance decay rate, scalar field structure, and time evolution of statistical moments confirm that there are two distinct regimes of scalar decay: a locally controlled regime, which applies when the domain size is comparable to the characteristic length scale of the velocity field, and a globally controlled regime, which applies when the domain is larger. Asymptotic predictions for the variance decay rate in both regimes show excellent agreement with the numerical results. Consideration of both the forward flow and its time reverse makes it possible to compare the scalar evolution in flows with one or two expanding directions; simulations confirm the theoretical prediction that the decay rate of the scalar is the same in both flows, despite the very different scalar field structures.

Streaming by leaky surface acoustic waves

Acoustic streaming, the generation of mean flow by dissipating acoustic waves, provides a promising method for flow pumping in microfluidic devices. In recent years, several groups have been experimenting with acoustic streaming induced by leaky surface waves: (Rayleigh) surface waves excited in a piezoelectric solid interact with a small volume of fluid where they generate acoustic waves and, as result of the viscous dissipation of these waves, a mean flow. We discuss the computation of the corresponding Lagrangian mean flow, which controls the trajectories of fluid particles and hence the mixing properties of the flows generated by this method. The problem is formulated using the averaged vorticity equation which extracts the dominant balance between wave dissipation and mean-flow dissipation. Particular attention is paid to the thin boundary layer that forms at the solid/liquid interface, where the flow is best computed using matched asymptotics. This leads to an explicit expression for a slip velocity, which includes the effect of the oscillations of the boundary. The Lagrangian mean flow is naturally separated into three contributions: an interior-driven Eulerian mean flow, a boundary-driven Eulerian mean flow and the Stokes drift. A scale analysis indicates that the latter two contributions can be neglected in devices much larger than the acoustic wavelength but need to be taken into account in smaller devices. A simple two-dimensional model of mean flow generation by surface acoustic waves is discussed as an illustration.

Estimating generalized Lyapunov exponents for products of random matrices

We discuss several techniques for the evaluation of the generalized Lyapunov exponents which characterize the growth of products of random matrices in the large-deviation regime. A Monte Carlo algorithm that performs importance sampling using a simple random resampling step is proposed as a general-purpose numerical method which is both efficient and easy to implement. Alternative techniques complementing this method are presented. These include the computation of the generalized Lyapunov exponents by solving numerically an eigenvalue problem, and some asymptotic results corresponding to high-order moments of the matrix products. Taken together, the techniques discussed in this paper provide a suite of methods which should prove useful for the evaluation of the generalized Lyapunov exponents in a broad range of applications. Their usefulness is demonstrated on particular products of random matrices arising in the study of scalar mixing by complex fluid flows.

Stokes-multiplier expansion in an inhomogeneous differential equation with a small parameter

Accurate approximations to the solutions of a second-order inhomogeneous equation with a small parameter ϵ are derived using exponential asymptotics. The subdominant homogeneous solutions that are switched on by an inhomogeneous solution through a Stokes phenomenon are computed. The computation relies on a resurgence relation, and it provides the ϵ -dependent Stokes multiplier in the form of a power series. The ϵ -dependence of the Stokes multiplier is related to constants of integration that can be chosen arbitrarily in the WKB-type construction of the homogeneous solution.

The equation under study governs the evolution of special solutions of the Boussinesq equations for rapidly rotating, strongly stratified fluids. In this context, the switching on of subdominant homogeneous solutions is interpreted as the generation of exponentially small inertia–gravity waves.

[Depression, anxiety and coping strategies in adult patients with cystic fibrosis]

The considerable progress that has been made in the treatment of cystic fibrosis has significantly increased life expectancy. The multi-disciplinary approach is now considered to be a priority by centers providing care for adults with cystic fibrosis. The aim of this study was to investigate three psychological morbidities that are commonly present with this disease: depression, anxiety and poor coping mechanisms for stress. Sixteen subjects (aged 19 to 37 years) participated in this study and were divided in three groups according to the severity of their pulmonary disease. Assessments of depression and anxiety were made from two perspectives: 1) the subject's own perception of his/her depressive and anxious state; 2) a psychologist's assessment of the patients depressive and anxious state. Then, reactions to stress were explored by analyzing "coping" strategies employed. Results indicate that patients underestimated the level of their depressive and anxious state when compared to the psychologists assessment. The majority of them exhibited "coping" strategies based on emotional responses. Levels of anxiety and depression did not show any relationship with the severity of pulmonary disease suggesting that the major determinant of emotional well-being lies with the individual's own perception of their state and of the support available to them.

Shunting normal pressure hydrocephalus: the predictive value of combined clinical and CT data

The value of an ordinal global scale derived from combined clinical and CT data (clin/CT scale) to predict the clinical outcome in 112 patients shunted for presumed normal pressure hydrocephalus (NPH) was analysed. The clinical data were retrospectively collected, all CT scans were re-evaluated, and the clin/CT scale was determined blind to the results of further ancillary tests and to the post-surgical outcome. The scale ranked three classes of prediction: on the basis of clinical and CT characteristics, improvement after shunting was probable, possible, or improbable. The predictive value of the clin/CT scale for the subgroup of communicating NPH was established for two different strategies, depending on the strictness of selection criteria for shunting. In the subgroup of patients with presumed communicating NPH, the prevalence of shunt responsiveness was 29%; the best strategy was to shunt only patients with probable shunt-responsive NPH: the sensitivity was 0.54, the specificity 0.84, and the predictive accuracy 0.75, with a limited number of ineffective shunts (11%) and missed improvements (13%). The study illustrates its need to assess the pre-test probability of NPH based on combined clinical and CT data, before establishing the clinical usefulness of an ancillary test.

Normal-pressure hydrocephalus. Is cisternography still useful in selecting patients for a shunt?

The clinical usefulness of cisternography in selecting patients with presumed normal-pressure hydrocephalus for shunting was investigated in 76 patients. The predictive value of a scale based on combined clinical and computed tomographic criteria was first established, followed by an assessment of the predictive value of cisternography. Predictions based on cisternograms were identical to those of the clinical/computed tomographic scale in 43%, better in 24%, and worse in 33%. Our findings suggest that cisternography does not improve the diagnostic accuracy of combined clinical and computed tomographic criteria in patients with presumed normal-pressure hydrocephalus.

The tarsal tunnel syndrome after a proximal lesion

Three patients in whom the first symptoms of the tarsal tunnel syndrome (TTS) emerged after an acute event proximal to but not affecting the ankle are described. These patients suggest that a pre-existing asymptomatic TTS may become manifest after a mechanism akin to that described in the "double crush" syndrome.

Shunting normal-pressure hydrocephalus: do the benefits outweigh the risks? A multicenter study and literature review

We performed a multicenter retrospective study in 166 consecutive patients shunted for presumed normal-pressure hydrocephalus (NPH) in the four neurosurgical departments of Amsterdam. Overall improvement occurred in 36%, substantial improvement in 21%. In the subgroup of idiopathic NPH (N = 127), marked improvement was only 15%. The incidence of shunt-responsive NPH in our area was 2.2/million/year. The rate of severe and moderate shunt-related complications was 28%, leading to death or severe residual morbidity in 7%. The substantial benefit/serious harm ration in the whole group was only three (21%/7%), decreasing to 1.7 in idiopathic NPH. By excluding patients at high surgical risk, this ratio might have risen to 10 in the whole group and to six in idiopathic NPH. Our experience is much less favorable than that encountered in the literature, reporting overall improvement in 74% and marked improvement in 55% of the shunted patients. We conclude that NPH is probably a very rare and still overdiagnosed syndrome and that the overall morbidity rate for each patient demonstrating meaningful improvement is high.

Normal pressure hydrocephalus: did publications alter management?

Forty six Dutch neurologists and neurosurgeons were interviewed to evaluate the clinical value of research articles on normal pressure hydrocephalus (NPH). From this survey it appears that most clinicians still limit investigations to psychometry, CSF-tap test(s), and cisternography. The main reasons for not using other techniques were: their invasiveness, technical complexity, poor availability, lack of time and doubt on their additional predictive value. There is an obvious discrepancy between the quantity of publications on NPH and their impact and their ability to assist clinicians in selecting potential NPH patients for a shunt.

Chronic spinal arachnoiditis following intracranial subarachnoid haemorrhage

A 54-year-old woman presented with progressive gait imbalance and increased urinary frequency, associated with spinal arachnoiditis. The symptoms started after the occurrence of communicating hydrocephalus as a sequel of subarachnoid haemorrhage (SAH), and were initially attributed to post-SAH vasospasm, decompensating hydrocephalus and/or periventricular leuko-encephalopathy. Further clinical deterioration led to the diagnosis of thoracic spinal arachnoiditis, as a second complication of SAH.

Non-tumoural aqueduct stenosis and normal pressure hydrocephalus in the elderly

From 1981 to 1985 a prospective study on normal pressure hydrocephalus was performed. One of the aims of this study was to determine the site of CSF obstruction. Among 17 consecutive patients with a tentative diagnosis of normal pressure hydrocephalus, nine appeared to have non-communicating hydrocephalus most probably due to primary non-tumoural aqueduct stenosis. This unexpected finding provides evidence that non-tumoural aqueduct stenosis is a frequent cause of normal pressure hydrocephalus in older patients. Some clinical, aetiological and therapeutic aspects in this particular subgroup are discussed.

The microenvironment of the spinal ganglion neuron in the rat during aging

The environment and particularly the glial sheath of the spinal ganglion neurons was systematically studied by light and electron microscopy in the young and senescent rat. Experiments using radioactive tracers tested the consequences of the functional perturbations associated with structural impairments. The results suggested the possibility that the glial sheath and the neuron aged differently. Whereas the glial sheath maintained its functional capacity relatively intact, neuronal performance was markedly and more rapidly impeded. The morphology and volume of the extracellular space were unchanged. Therefore, impairment of the glioneuronal units in the spinal ganglion during aging cannot be assigned to environmental and vascular phenomena.

CT scans suggestive of tumour in multiple sclerosis

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Mitochondrial alterations in the spinal ganglion neurons in ageing rats

An ultrastructural study of the mitochondria was performed in the 3-, 24-, and 32-month-old rats. Accumulation of "unusual" substances or structures was the most striking characteristic in senescent neuron mitochondria. Tubular or filamentous inclusions, modifications in matrix density, deposit of glycogen particles and electron-dense globules were observed. The various nature of these alterations and their different situation in the cristae or in the matrix, suggested that they could be the result of some specific oxidative metabolism dysfunctions associated with ageing.

Ageing of the spinal ganglion neurons in the rat: a radioautographic study following injection of [3H]lysine

After administration of [3H]lysine to 3- and 24-month-old rats, radioautography demonstrates a significantly less important uptake in the A-type spinal ganglion neurons and in the old animals. This is in agreement with the existence of at least two functional categories of neurons in the spinal ganglion and suggests that protein synthesis is diminished in the old animals. The very fact that incorporation varies between animals of the same age sustains the hypothesis according to which amplitude of ageing is essentially an individual physiological-dependent process.