Full reciprocal-space mapping up to 2000†K under controlled atmosphere: the multipurpose QMAX furnace.

A furnace that covers the temperature range from room temperature up to 2000 K has been designed, built and implemented on the D2AM beamline at the ESRF. The QMAX furnace is devoted to the full exploration of the reciprocal hemispace located above the sample surface. It is well suited for symmetric and asymmetric 3D reciprocal space mapping. Owing to the hemispherical design of the furnace, 3D grazing-incidence small- and wide-angle scattering and diffraction measurements are possible. Inert and reactive experiments can be performed at atmospheric pressure under controlled gas flux. It is demonstrated that the QMAX furnace allows monitoring of structural phase transitions as well as microstructural evolution at the nanoscale, such as self-organization processes, crystal growth and strain relaxation. A time-resolved in situ oxidation experiment illustrates the capability to probe the high-temperature reactivity of materials.

Self-organized arrays of dislocations in thin smectic liquid crystal films.

Combining optical microscopy, synchrotron X-ray diffraction and ellipsometry, we studied the internal structure of linear defect domains (oily streaks) in films of a smectic liquid crystal 8CB with thicknesses in the range of 100-300 nm. These films are confined between air and a rubbed PVA polymer substrate which imposes hybrid anchoring conditions (normal and unidirectional planar, respectively). We show how the presence or absence of dislocations controls the structure of highly deformed thin smectic films. Each domain contains smectic layers curved in the shape of flattened hemicylinders to satisfy both anchoring conditions, together with grain boundaries whose size and shape are controlled by the presence of dislocation lines. A flat grain boundary normal to the interface connects neighboring hemicylinders, while a rotating grain boundary (RGB) is located near the axis of curvature of the cylinders. The RGB shape appears such that dislocation lines are concentrated at its summit close to the air interface. The smectic layers reach the polymer substrate via a transition region where the smectic layer orientation satisfies the planar anchoring conditions over the entire polymer substrate and whose thickness does not depend on that of the film. The strength of planar anchoring appears to be high, larger than 10(-2) mJ m(-2), compensating for the high energy cost of creating an additional 2D defect between a horizontal smectic layer and perpendicular ones of the transition region. This 2D defect may be melted, in order to avoid the creation of a transition region structure composed of a large number of dislocations. As a result, linear defect domains can be considered as arrays of oriented defects, straight dislocations of various Burger vectors, whose location is now known, and 2D nematic defects. The possibility of easy variation between the present structure with a moderate amount of dislocations and a structure with a large number of dislocations is also demonstrated.

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.

The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.

Polarization Rotation in Ferroelectric Tricolor PbTiO3/SrTiO3/PbZr0.2Ti0.8O3 Superlattices.

In ferroelectric thin films, controlling the orientation of the polarization is a key element to controlling their physical properties. We use laboratory and synchrotron X-ray diffraction to investigate ferroelectric bicolor PbTiO3/PbZr0.2Ti0.8O3 and tricolor PbTiO3/SrTiO3/PbZr0.2Ti0.8O3 superlattices and to study the role of the SrTiO3 layers on the domain structure. In the tricolor superlattices, we demonstrate the existence of 180° ferroelectric stripe nanodomains, induced by the depolarization field produced by the SrTiO3 layers. Each ultrathin SrTiO3 layer modifies the electrostatic boundary conditions between the ferroelectric layers compared to the corresponding bicolor structures, leading to the suppression of the a/c polydomain states. Combined with the electrostatic effect, the tensile strain induced by PbZr0.2Ti0.8O3 in the PbTiO3 layers leads to polarization rotation in the system as evidenced by grazing incidence X-ray measurements. This polarization rotation is associated with the monoclinic Mc phase as revealed by the splitting of the (HHL) and (H0L) reciprocal lattice points. This work demonstrates that the tricolor paraelectric/ferroelectric superlattices constitute a tunable system to investigate the concomitant effects of strains and depolarizing fields. Our studies provide a pathway to stabilize a monoclinic symmetry in ferroelectric layers, which is of particular interest for the enhancement of the piezoelectric properties.

High energy resolution five-crystal spectrometer for high quality fluorescence and absorption measurements on an x-ray absorption spectroscopy beamline.

Fluorescence detection is classically achieved with a solid state detector (SSD) on x-ray absorption spectroscopy (XAS) beamlines. This kind of detection however presents some limitations related to the limited energy resolution and saturation. Crystal analyzer spectrometers (CAS) based on a Johann-type geometry have been developed to overcome these limitations. We have tested and installed such a system on the BM30B/CRG-FAME XAS beamline at the ESRF dedicated to the structural investigation of very dilute systems in environmental, material and biological sciences. The spectrometer has been designed to be a mobile device for easy integration in multi-purpose hard x-ray synchrotron beamlines or even with a laboratory x-ray source. The CAS allows to collect x-ray photons from a large solid angle with five spherically bent crystals. It will cover a large energy range allowing to probe fluorescence lines characteristic of all the elements from Ca (Z = 20) to U (Z = 92). It provides an energy resolution of 1-2 eV. XAS spectroscopy is the main application of this device even if other spectroscopic techniques (RIXS, XES, XRS, etc.) can be also achieved with it. The performances of the CAS are illustrated by two experiments that are difficult or impossible to perform with SSD and the complementarity of the CAS vs SSD detectors is discussed.

Detective quantum efficiency, modulation transfer function and energy resolution comparison between CdTe and silicon sensors bump-bonded to XPAD3S.

XPAD3S is a single-photon-counting chip developed in collaboration by SOLEIL Synchrotron, the Institut Louis Néel and the Centre de Physique de Particules de Marseille. The circuit, designed in the 0.25 microm IBM technology, contains 9600 square pixels with 130 microm side giving a total size of 1 cm x 1.5 cm. The main features of each pixel are: single threshold adjustable from 4.5 keV up to 35 keV, 2 ms frame rate, 10(7) photons s(-1) mm(-2) maximum local count rate, and a 12-bit internal counter with overflow allowing a full 27-bit dynamic range to be reached. The XPAD3S was hybridized using the flip-chip technology with both a 500 microm silicon sensor and a 700 microm CdTe sensor with Schottky contacts. Imaging performances of both detectors were evaluated using X-rays from 6 keV up to 35 keV. The detective quantum efficiency at zero line-pairs mm(-1) for a silicon sensor follows the absorption law whereas for CdTe a strong deficit at low photon energy, produced by an inefficient entrance layer, is measured. The modulation transfer function was evaluated and it was shown that both detectors present an ideal modulation transfer function at 26 keV, limited only by the pixel size. The influence of the Cd and Te K-edges of the CdTe sensor was measured and simulated, establishing that fluorescence photons reduce the contrast transfer at the Nyquist frequency from 60% to 40% which remains acceptable. The energy resolution was evaluated at 6% with silicon using 16 keV X-rays, and 8% with CdTe using 35 keV X-rays. A 7 cm x 12 cm XPAD3 imager, built with eight silicon modules (seven circuits per module) tiled together, was successfully used for X-ray diffraction experiments. A first result recently obtained with a new 2 cm x 3 cm CdTe imager is also presented.

New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides.

BACKGROUND: Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the Sitopsis section, having Aegilops speltoides (SS, 2n = 14) as the closest identified relative. However molecular relationships based on genomic sequence comparison, including both coding and non-coding DNA, have never been investigated. In an attempt to clarify these relationships, we compared, in this study, sequences of the Storage Protein Activator (SPA) locus region of the S genome of Ae. speltoides (2n = 14) to that of the A, B and D genomes co-resident in the hexaploid wheat species (Triticum aestivum, AABBDD, 2n = 42). RESULTS: Four BAC clones, spanning the SPA locus of respectively the A, B, D and S genomes, were isolated and sequenced. Orthologous genomic regions were identified as delimited by shared non-transposable elements and non-coding sequences surrounding the SPA gene and correspond to 35,268, 22,739, 43,397 and 53,919 bp for the A, B, D and S genomes, respectively. Sequence length discrepancies within and outside the SPA orthologous regions are the result of non-shared transposable elements (TE) insertions, all of which inserted after the progenitors of the four genomes divergence. CONCLUSION: On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, Ae speltoides appears to be more evolutionary related to the B genome of T. aestivum than the A and D genomes. However, the differential insertions of TEs, none of which are conserved between the two genomes led to the conclusion that the S genome of Ae. speltoides has diverged very early from the progenitor of the B genome which remains to be identified.

Troika II: a versatile beamline for the study of liquid and solid interfaces.

The Troika II beamline at the European Synchrotron Radiation Facility was conceived as a versatile beamline for the study of liquid and solid interfaces, combining grazing-incidence diffraction, X-ray reflectivity and grazing-incidence small-angle scattering in a single instrument. Scattering experiments can be performed both in horizontal and in vertical scattering geometry. Additional options are the use of analyzer crystals for high-resolution studies in both the horizontal and the vertical scattering geometry as well as the use of a horizontal microfocusing mirror for experiments requiring very high flux onto the sample. Here, the way in which the features of the beamline have been exploited in selected recent experiments is described.

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.

DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes.

The model genome of Arabidopsis thaliana contains a DEAD-box RNA helicase family (RH) of 58 members, i.e. almost twice as many as in the animal or yeast genomes. Transcript profiling using real-time quantitative polymerase chain reaction (PCR) has been obtained for 20 AtRHs from nine different organs. Two AtRHs exhibited plant-specific profiles associated with photosynthetic and sink organs. The other 18 AtRHs had the same transcript profile, and the levels of transcription of these 'housekeeping'AtRHs were under strict quantitative control over a large range of values. Transcript levels may be very different between the most recently duplicated genes. The master regulatory element in the definition of the transcript level is the simultaneous presence of a TATA-box and an intron in the 5' untranslated region (UTR). There is a positive and highly significant correlation between the size of the 5' UTR intron and the transcription level, as long as a characteristic TATA-box is present. Our work on the housekeeping AtRHs suggests a scenario for the evolution of duplicated genes, leading to both highly and poorly transcribed genes in the same terminal branch of the phylogenetic tree. The general evolutionary drive of the AtRH family, after duplication of a highly transcribed ancestral AtRH, was towards an alteration of the transcriptional activity of the divergent duplicates through successive events of suppression of the TATA-box and/or the 5' UTR intron.

Introns in, introns out in plant gene families: a genomic approach of the dynamics of gene structure.

Gene duplication is considered to be a source of genetic information for the creation of new functions. The Arabidopsis thaliana genome sequence revealed that a majority of plant genes belong to gene families. Regarding the problem of genes involved in the genesis of novel organs or functions during evolution, the reconstitution of the evolutionary history of gene families is of critical importance. A comparison of the intron/exon gene structure may provide clues for the understanding of the evolutionary mechanisms underlying the genesis of gene families. An extensive study of A. thaliana genome showed that families of duplicated genes may be organized according to the number and/or density of intron and the diversity in gene structure. In this paper, we propose a genomic classification of several A. thaliana gene families based on introns in an evolutionary perspective.