Evidence for Differences in the Temporal Progress of Plasmopara viticola Clades riparia and aestivalis Airborne Inoculum Monitored in Vineyards in Eastern Canada Using a Specific Multiplex Quantitative PCR Assay.

Four clades of Plasmopara viticola isolated from wild and cultivated Vitis species were described in 2013. Only P. viticola clades riparia and aestivalis have been detected in eastern Canada. To increase our understanding of the epidemiology of these clades of P. viticola, airborne sporangia were monitored with spore samplers at two experimental vineyards from 2015 to 2018 and at 11, 14, and 15 commercial vineyards in 2016, 2017, and 2018, respectively. At each vineyard and in each year, airborne sporangia were assessed three times weekly from grapevine budbreak to harvest. To accurately monitor airborne inoculum, a specific and sensitive quantitative PCR assay for simultaneous quantification of P. viticola clades riparia and aestivalis was developed. At the experimental site, in the vineyard planted with the hybrid grape variety Chancellor, mostly P. viticola clade riparia was detected. In vineyards planted with multiple grape varieties, airborne sporangia of P. viticola clade riparia were prevalent at the beginning of the season, whereas P. viticola clade aestivalis was mostly detected from midseason to harvest. At the commercial sites, airborne sporangia of P. viticola clade riparia were more prevalent in 2016, whereas P. viticola clade aestivalis was more prevalent in 2017 and 2018. The only significant difference between the inoculum progress curves was the time at which 50% of the seasonal inoculum was reached, with an average for the 3 years of 100.8 and 117.9 days since 1 May for P. viticola clade riparia and clade aestivalis, respectively. When airborne sporangium concentrations were expressed as the proportion of the two clades, in general, the proportion of clade aestivalis to that of clade riparia was low at the beginning of the season and increased to reach approximately 0.9 to 1.0 at the end of the season. These results suggest that both clades of P. viticola coexist, but that clade aestivalis is predominant and that downy mildew epidemics caused by P. viticola clade riparia occur 2 to 3 weeks before those caused by clade aestivalis.

High-reflectance magnetron-sputtered scandium-based x-ray multilayer mirrors for the water window.

We present an experimental comparison of several Sc-based short period multilayer mirrors including Cr/Sc with B4C barrier layers and CrNx/Sc, and we propose a new material combination that provides high reflectance in the water window domain. Multilayer samples with period thickness in the range 1.5-1.7 nm have been deposited by magnetron sputtering and characterized by x-ray reflectometry with a Cu-Kα source and with synchrotron radiation near the Sc-L2,3 edge. Best results are achieved by combining the nitridation of Cr layers and the addition of B4C barrier layers. Near normal incidence reflectance as high as 23% has been measured at photon energy of 397 eV. A simulation model of the multilayer structure is proposed and it predicts that reflectance higher than 32% is achievable with CrNx/B4C/Sc mirrors.

The LUCIA beamline at SOLEIL.

Commissioned in May 2004 on the SLS machine, the LUCIA beamline was moved to the synchrotron SOLEIL during the summer of 2008. To take advantage of this new setting several changes to its design were introduced. Here, a review of the various improvements of the mechanics and, mostly, of the optics is given. Described in detail are the results of a new multilayer grating monochromator implemented on the Kohzu vessel already holding the two-crystal set-up. It consists of a grating grooved onto a multilayer (replacing the first crystal) associated to a multilayer (as a second crystal). It allows a shift of the low-energy limit of the beamline to around 500 eV with an energy resolution and a photon flux comparable with those of the previous couples of crystals (KTP and beryl).

X-ray broadband Ni/SiC multilayers: improvement with W barrier layers.

We present an experimental study and performance improvement of periodic and aperiodic Ni/SiC multilayer coatings. Periodic Ni/SiC multilayer mirrors have been coated and characterized by grazing incidence X-ray reflectometry at 8.048 keV (Cu Kα radiation) and by measurements at 3 keV and 5 keV on synchrotron radiation facilities. An interdiffusion effect is found between Ni and SiC layers. A two-material model, Ni(x)Si(y)/SiC, using a silicide instead of Ni, was used to fit the measurements. The addition of 0.6 nm W barrier layers at the interfaces allows a significant reduction of the interdiffusion between Ni and SiC. In order to obtain a specific reflectivity profile in the 2 - 8 keV energy range, we have designed and coated aperiodic multilayer mirrors by using Ni/SiC with and without W barrier layers. The experimental reflectivity profiles as a function of the photon energy were measured on a synchrotron radiation facility in both cases. Adding W barrier layers in Ni/SiC multilayers provides a better precision on the layer thicknesses and a very good agreement between the experimental data and the targeted spectral profile.

How to focus an attosecond pulse.

Attosecond experiments involving focusing of attosecond light pulses can suffer from a spread of the attosecond radiation both in space and time due to optical aberrations. We present a detailed numerical study of the distortions induced in the most common focusing geometries that make use of parabolic, spherical, toroidal and ellipsoidal mirrors. We deduce the consequences on the pulse duration and possible issues that could arise in applications of attosecond pulses. This should serve as a guideline for setting up attosecond focusing optics.

Design and simulation of multilayer coatings for a multi-channel Wolter-like x-ray imager with large field of view and high resolution.

X-ray diagnostics are key instruments for understanding the physics behind inertial confinement fusion experiments. We report on the multilayer design optimization for the Toroidal X-ray Imager (TXI), a hard x-rays microscope instrument designed by Commissariat à l'énergie atomique (CEA) and Laboratoire Charles Fabry (LCF) to be installed on the National Ignition Facility. TXI includes six channels designed for three different energy bands centered on 8.7, 13, and 17.5 keV. Each channel is made up of two toroidal mirrors arranged in a Wolter-like configuration. The required field of view is 800 × 400 µm2, and the resolution should be better than 5 µm. In addition, we seek to estimate the spatial distribution of the temperature, which requires no spectral overlap of the different energy bands and a good spectral homogeneity of the image produced. The development of the multilayer coatings was performed in a two-step method. First, the coatings were optimized to obtain proper energy bands. Then, an x-ray tracing code was used to calculate the integrated optical response of each channel and adjust the response of the mirror to fulfill the requirements. To fulfill all the specifications, we propose an original design using a combination of two aperiodic coatings, one with a narrow bandwidth and the other one with a larger bandwidth.

A 2-4 keV multilayer mirrored channel for the NIF Dante system.

During inertial confinement fusion experiments at the National Ignition Facility (NIF), a capsule filled with deuterium and tritium (DT) gas, surrounded by a DT ice layer and a high-density carbon ablator, is driven to the temperature and densities required to initiate fusion. In the indirect method, 2 MJ of NIF laser light heats the inside of a gold hohlraum to a radiation temperature of 300 eV; thermal x rays from the hohlraum interior couple to the capsule and create a central hotspot at tens of millions degrees Kelvin and a density of 100-200 g/cm3. During the laser interaction with the gold wall, m-band x rays are produced at ∼2.5 keV; these can penetrate into the capsule and preheat the ablator and DT fuel. Preheat can impact instability growth rates in the ablation front and at the fuel-ablator interface. Monitoring the hohlraum x-ray spectrum throughout the implosion is, therefore, critical; for this purpose, a Multilayer Mirror (MLM) with flat response in the 2-4 keV range has been installed in the NIF 37° Dante calorimeter. Precision engineering and x-ray calibration of components mean the channel will report 2-4 keV spectral power with an uncertainty of ±8.7%.

Characterization of single-nucleotide-polymorphism markers for Plasmopara viticola, the causal agent of grapevine downy mildew.

We report 34 new nuclear single-nucleotide-polymorphism (SNP) markers that have been developed from an expressed sequence tag library of Plasmopara viticola, the causal agent of grapevine downy mildew. This newly developed battery of markers will provide useful additional genetic tools for population genetic studies of this important agronomic species.

Duration of ultrashort pulses in the presence of spatio-temporal coupling.

We report on a simple method allowing one to decompose the duration of arbitrary ultrashort light pulses, potentially distorted by space-time coupling, into four elementary durations. Such a decomposition shows that, in linear optics, a spatio-temporal pulse can be stretched with respect to its Fourier limit by only three independent phenomena: nonlinear frequency dependence of the spectral phase over the whole spatial extent of the pulse, spectral amplitude inhomogeneities in space, and spectral phase inhomogeneities in space. We illustrate such a decomposition using numerical simulations of complex spatio-temporal femtosecond and attosecond pulses. Finally we show that the contribution of two of these three effects to the pulse duration is measurable without any spectral phase characterization.

Control of the attosecond synchronization of XUV radiation with phase-optimized mirrors.

We report on the advanced amplitude and phase control of attosecond radiation allowed by specifically-designed multilayer XUV mirrors. We first demonstrate that such mirrors can compensate for the intrinsic chirp of the attosecond emission over a large bandwidth of more than 20 eV. We then show that their combination with metallic foils introduces a third-order dispersion that is adjustable through the mirror's incidence angle. This results in a controllable beating allowing the radiation to be shaped from a single to a series of sub-100 as pulses.

Productivity, water-use efficiency and tolerance to moderate water deficit correlate in 33 poplar genotypes from a Populus deltoides x Populus trichocarpa F1 progeny.

Genotypic variability for productivity, water-use efficiency and leaf traits in 33 genotypes selected from an F1 progeny of Populus deltoides Bartr. ex Marsh x Populus trichocarpa L. was explored under optimal and moderate water-deficit conditions. Saplings of the 33 genotypes were grown in a two-plot open field at INRA Orléans (France) and coppiced every year. A moderate water deficit was induced during two successive years on one plot by withholding irrigation, while the second one remained irrigated (control). Stem biomass and leaf structure (e.g., specific leaf area and leaf area) were measured in 2004 and 2005 and functional leaf traits (e.g., carbon isotope discrimination, Delta) were measured only in 2004. Tolerance to water deficit was estimated at genotype level as the ability to limit losses in biomass production in water deficit versus control trees. Stem biomass, leaf structure and Delta displayed a significant genotypic variability whatever the irrigation regime. For all traits, genotype ranks remained stable across years for similar irrigation conditions. Carbon isotope discrimination scaled negatively with productivity and leaf nitrogen content in controls. The most productive genotypes were the least tolerant to moderate water deficit. No relationship was evidenced between Delta and the level of tolerance to water deficit. The relationships between traits evidenced in this collection of P. deltoides x P. trichocarpa F1 genotypes contrast with the ones that were previously detected in a collection of P. deltoides x Populus nigra L. cultivars tested in the same field trial.

Tempo and mode of early gene loss in endosymbiotic bacteria from insects.

BACKGROUND: Understanding evolutionary processes that drive genome reduction requires determining the tempo (rate) and the mode (size and types of deletions) of gene losses. In this study, we analysed five endosymbiotic genome sequences of the gamma-proteobacteria (three different Buchnera aphidicola strains, Wigglesworthia glossinidia, Blochmannia floridanus) to test if gene loss could be driven by the selective importance of genes. We used a parsimony method to reconstruct a minimal ancestral genome of insect endosymbionts and quantified gene loss along the branches of the phylogenetic tree. To evaluate the selective or functional importance of genes, we used a parameter that measures the level of adaptive codon bias in E. coli (i.e. codon adaptive index, or CAI), and also estimates of evolutionary rates (Ka) between pairs of orthologs either in free-living bacteria or in pairs of symbionts. RESULTS: Our results demonstrate that genes lost in the early stages of symbiosis were on average less selectively constrained than genes conserved in any of the extant symbiotic strains studied. These results also extend to more recent events of gene losses (i.e. among Buchnera strains) that still tend to concentrate on genes with low adaptive bias in E. coli and high evolutionary rates both in free-living and in symbiotic lineages. In addition, we analyzed the physical organization of gene losses for early steps of symbiosis acquisition under the hypothesis of a common origin of different symbioses. In contrast with previous findings we show that gene losses mostly occurred through loss of rather small blocks and mostly in syntenic regions between at least one of the symbionts and present-day E. coli. CONCLUSION: At both ancient and recent stages of symbiosis evolution, gene loss was at least partially influenced by selection, highly conserved genes being retained more readily than lowly conserved genes: although losses might result from drift due to the bottlenecking of endosymbiontic populations, we demonstrated that purifying selection also acted by retaining genes of greater selective importance.

The binding of N-trifluoroacetyl chito-oligosaccharides to wheat-germ agglutinin: a fluorescence investigation.

We describe the synthesis of N-trifluoroacetyl chito-oligosaccharides and their use as ligands to probe the binding sites of wheat-germ agglutinin, a lectin specific for N-acetylglucosamine. The binding is monitored using intrinsic protein fluorescence, which is due to tryptophan side-chains. We present arguments purporting to show the presence of a fluorophore close to each of the four sites. The binding of chito-oligosaccharides to wheat-germ agglutinin is complex and can only be approximately described by an independent and equivalent sites model. This model applies when the ligand concentration range is restricted to higher values. The possible role of ligand-mediated protein aggregation and of site inequivalence is discussed. We find that the affinity of trifluoroacetylated chito-oligosaccharides for wheat-germ agglutinin is higher than that of the N-acetylated parent compounds, the difference increasing with chain length. Our results are in agreement with a model of the binding site previously proposed by Clegg et al. (Biochemistry 22 (1983) 4797-4804).

Purification of an alpha-L-fucoside-binding protein from Rhizobium lupini.

Lectins associated with the bacterial cell surface of Rhizobium lupini strain LL13 were evidenced by erythrocyte agglutination, by aggregation of neoglycoprotein coated beads and by spectrofluorimetry using fluoresceinylated neoglycoproteins. At pH 5.0, a specific binding of the fluorescein-labelled neoglycoprotein bearing alpha-L-fucose was observed. The binding of this labelled neoglycoprotein is a saturable phenomenon and is inhibited by the same unlabelled neoglycoprotein. Extracts of R lupini obtained by disrupting a bacterial pellet through a French press were stabilized at pH 5.6 by gel filtration and purified to homogeneity by affinity chromatography on Agarose A4 substituted with alpha-L-fucose. A protein with a M(r) approximately 19,000 was specifically eluted from this affinity column with L-fucose. Isoelectric focusing of this sample yielded a single band with pI near 6.7. This protein specifically aggregated L-Fuc-BSA-coated microspheres. The results obtained in the present study indicate that we have purified from Rhizobium lupini strain LL13, a L-fucose binding protein as a lectin.

Alkylsyringamides, new inducers of Agrobacterium tumefaciens virulence genes.

The virulence genes of Agrobacterium tumefaciens are specifically activated by plant phenolic compounds and allow this organism to genetically transform plant cells. New types of phenolic compounds, three phenol amides derived from syringic acid, were synthesized. Introduction of an amide group in syringic acid strongly enhances its vir gene inducing activity.

Characterization of two galactosidases extracted from wheat germ with a hydroalcoholic solvent.

Alpha- and beta-D-galactosidases were characterized from a hydroalcoholic extract of wheat germ (Triticum vulgare). Kinetic constants (Vmax and KM) and the optimal pHs for the hydrolysis of p-nitrophenyl galactopyranosides by both enzymes were determined. These enzymes presented a high stability in hydroalcoholic medium and were inhibited by iodoacetamide and sodium p-hydroxy-mercuribenzoate.

Purification of two lectins from a nopalin Agrobacterium tumefaciens strain.

Lectins were evidenced on the surface of one Agrobacterium tumefaciens wild strain (82,139) by agglutination test and neoglycoprotein labelling. Bacteria were incubated in the presence of various fluorescein-labelled neoglycoproteins and the binding was assessed by a fluorimetric method. Among the fluorescein-labelled neoglycoproteins tested, the one bearing alpha-D-galactosyl residues was the most efficient. The labelling was optimal at pH 5.0 and naught at pH above 7. The binding was specifically inhibited by homologous fluorescein-free neoglycoproteins. A galactoside-specific lectin was purified to homogeneity by affinity chromatography on agarose-A4 substituted with alpha-D-galactopyranosyl residues. Upon polyacrylamide gel electrophoresis, a single band (M(r) 58,000) was detected. This alpha-D-galactoside-specific lectin agglutinated preferentially human B red blood cells at pH 5.0. Another lectin specific for alpha-L-rhamnoside (M(r) 40,000) not retained on the immobilised galactose was purified by affinity chromatography on alpha-L-rhamnosyl substituted agarose-A4. This L-rhamnoside-specific lectin preferentially agglutinated horse erythrocytes. On the basis of their M(r) and on their sugar specificity, these two lectins are novel lectins with regard to the known sugar-binding proteins present in the Rhizobiaceae family: Agrobacterium, Rhizobium or Bradyrhizobium strains.

Microsatellite allele sizing: difference between automated capillary electrophoresis and manual technique.

By comparing data collected with different automated sequencers and a manual technique (fragment separation in a silver-stained polyacrylamide gel), we found strong discrepancies in allele size of microsatellite loci. To quantify the sizing bias generated by automated capillary electrophoresis, we typed 51 alleles at seven loci andfound that differences between actual (manual) and called (automated) sizing were inversely related to locus size. This result seems independent of the fluorescent dye but might be due to different migration patterns of the size standard and the microsatellite loci. Thus, it is essential to distinguish between actual (that can only be confirmed by sequencing) and called (obtained with automated sequencer) allele sizes. To enable the comparison of data collected by different laboratories on different instruments, the greatest attention should be paid to material and protocol descriptions used for allele sizing, and reference standard DNA genotypes should be shared between collaborating laboratories. Without these precautions, scoring errors in allele size might result in important misleading conclusions.

Multiple routes to asexuality in an aphid species.

Cyclical parthenogens, including aphids, are important models for studying the evolution of sex. However, little is known about transitions to asexuality in aphids, although the mode of origin of asexual lineages has important consequences for their level of genetic diversity, ecological adaptability and the outcome of competition with their sexual relatives. Thus, we surveyed nuclear, mitochondrial and biological data obtained on cyclical and obligate parthenogens of the bird cherry-oat aphid, Rhopalosiphum padi (L), to investigate the frequency of transitions from sexuality to permanent asexuality. Many instances of asexual lineages retaining the ability to produce males are known in aphids, so particular attention was paid to the existence of occasional matings between females from sexual lineages and males produced by asexual lineages, which have the potential to produce new asexual lineages. Phylogenetic inference based on microsatellite and mitochondrial data indicates at least three independent origins of asexuality in R. padi, yielding the strongest evidence to date for multiple origins of asexuality in an aphid. Moreover, several lines of evidence demonstrate that transitions to asexuality result from two mechanisms: a complete spontaneous loss of sex and repeated gene flow from essentially asexual lineages into sexual ones.

Host and parasite population structure in a natural plant-pathogen system

We investigated the genetic population structure in a metapopulation of the plant Silene latifolia (Caryophyllaceae) and its fungal pathogen Microbotryum violaceum (Ustilaginales), a pollinator-borne disease. Population structure of the host plant was estimated using allozyme markers and that of the fungus by microsatellites. Both host and parasite showed significant differentiation, but parasite populations were 12 times more strongly differentiated than those of the hosts. We found significant isolation by distance for host populations but not for parasite populations. Higher population differentiation for the parasite may result from small effective population size, high selfing rates, or low migration rate. In this system, hosts are obligate outcrossers and they migrate by seeds and pollen, whereas parasites can self-fertilize and migrate only on pollinating insects. We discuss the effect of limited gene flow in this parasite on its coevolutionary interaction with its host, and its potential for local adaptation on sympatric host populations.