A compact-rigid multi-analyser for energy and angle filtering of high-resolution X-ray experiments. Part 2. Efficiency of a single-crystal-comb

Diffraction instruments using filtering by one or several analyser crystals exist since the 1980s and 1990s at synchrotron radiation sources, but, due to its low efficiency, this filtering is little used on laboratory sources. In order to overcome this limitation, the efficiency of a small diffraction filtering multi-analyzer block (MAD block) realized with a `single-crystal-comb' curved on a rigid support is demonstrated here. The geometry of this curved surface is logarithmic spiral and is optimized to allow multi-filtering over a relatively important diffraction angular range and to be also applicable over an X-ray spectral range. The efficiency of such a small rigid-compact MAD block consisting of this single-crystal-comb generating 20-50 Si(111) single-crystal blades, associated with a block of Soller collimators, is demonstrated. The angle between each crystal is 0.1°, so the measurement range of the comb is 2-5°. The geometry of this system has been optimized for operation with a synchrotron X-ray source over an energy range of 22 keV to 46 keV and could be used with laboratory X-ray sources (Ag Kα<sub>1</sub>, 22.1 keV). This MAD block complements and exploits the qualities of the `photon-counting' detectors which have very low intrinsic noise. Their joint efficacy is supported by powder pattern measurements of a LaB₆ reference sample and of several heterogeneous samples of cultural heritage materials, carried out at 22 keV on the D2AM beamline at the ESRF. Their signal-to-noise ratio is excellent (1000/1) and allows the detection thresholds of the measurements (from 3-1% to 0.1%) to detect minor phases in the studies of `real' heterogeneous materials to be drastically improved.

Observations of a streak texture in the hybrid-aligned smectic-C phase

A novel structure was observed below the smectic-A-smectic-C phase transition in a very thin open cell having an air interface above and enforced planar anchoring at the substrate below. The structure appears as periodic dark and light streaks running perpendicular to the oily streaks, which are present in the smectic-A phase [D. Coursault et al., Soft Matter, 2016, 12, 678]. These new streaks, which we call "soapy streaks", form by extending from one oily streak to the next in discrete steps, eliminating optical evidence at visible wavelengths of the oily streaks. At lower temperatures the streaks can undulate and exhibit a sawtooth-like structure; such a structure is chiral in two dimensions. A possible scenario for the origin of these streaks is presented.

Total synthesis of malagashanine: a chloroquine potentiating indole alkaloid with unusual stereochemistry

The first total synthesis of malagashanine, a chloroquine potentiating indole alkaloid, is presented. A highly stereoselective cascade annulation reaction was developed to generate the tetracyclic core of the Malagasy alkaloids. This chemistry is likely to be broadly applicable to the synthesis of other members of this stereochemically unique family of natural products.

Tuning the conductivity type in a room temperature magnetic oxide: Ni-doped Ga0.6Fe1.4O3 thin films

The mechanism responsible for conduction in pulsed laser deposited thin films of room temperature ferrimagnetic Ga_0.6Fe_1.4O₃ is fully elucidated. The conduction type can be tuned from n to p through doping with bivalent Ni ions.

K-edge imaging with the XPAD3 hybrid pixel detector, direct comparison of CdTe and Si sensors

We investigate the improvement from the use of high-Z CdTe sensors for pre-clinical K-edge imaging with the hybrid pixel detectors XPAD3. We compare XPAD3 chips bump bonded to Si or CdTe sensors in identical experimental conditions. Image performance for narrow energy bin acquisitions and contrast-to-noise ratios of K-edge images are presented and compared. CdTe sensors achieve signal-to-noise ratios at least three times higher than Si sensors within narrow energy bins, thanks to their much higher detection efficiency. Nevertheless Si sensors provide better contrast-to-noise ratios in K-edge imaging when working at equivalent counting statistics, due to their better estimation of the attenuation coefficient of the contrast agent. Results are compared to simulated data in the case of the XPAD3/Si detector. Good agreement is observed when including charge sharing between pixels, which have a strong impact on contrast-to-noise ratios in K-edge images.

Development of structural order during supercooling of a fragile oxide melt

The authors have studied the structural evolution of the fragile glass-forming liquid CaAl2O4 during supercooling from the stable liquid phase to the cold glass below Tg. The evolution is characterized by a sharpening of the first diffraction peak and a shortening of the average nearest-neighbor bond length around 1.25Tg, indicating an increase in the degree of both intermediate-range and short-range orders occurring close to the dynamical crossover temperature. The cooling curve developed a kink at this temperature, indicating a simultaneous change in thermodynamic properties.

Application of a hybrid pixel detector to powder diffraction

Results obtained using a hybrid pixel photon-counting detector in powder diffraction experiments are presented. The detector works at room temperature and its dynamic response ranges from 0.01 photons pixel(-1) s(-1) up to 10(6) photons pixel(-1) s(-1). The pixel sizes are 0.33 mm x 0.33 mm for a total area of 68 mm x 68 mm. On recording high-resolution diffraction patterns of powders, a reduction of the experimental time by more than a factor of 20 is obtained without loss of data quality. The example of an X-zeolite shows that such detectors can be used for very demanding anomalous experiments. In situ experiments of quenching liquid oxides show that frames of 0.01 s can be achieved for studying such processes.

A pixel detector with large dynamic range for high photon counting rates

In this paper, results obtained from a prototype photon counting detector are presented. The pixel size is 330 µm × 330 µm for a total area of 16 µm × 40 mm. The detector works at room temperature and its dynamic response ranges from 0.01 up to 106photons pixel−1s−1. An energy resolution of about 1.5 keV has been measured. Very encouraging small-angle X-ray scattering (SAXS) and diffraction patterns were obtained, demonstrating the success of the prototype. Plans for future developments based on this study are presented.

Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabditis, and Drosophila

The DEAD box RNA helicase (RH) proteins are homologs involved in diverse cellular functions in all of the organisms from prokaryotes to eukaryotes. Nevertheless, there is a lack of conservation in the splicing pattern in the 53 Arabidopsis thaliana (AtRHs), the 32 Caenorhabditis elegans (CeRHs) and the 29 Drosophila melanogaster (DmRHs) genes. Of the 153 different observed intron positions, 4 are conserved between AtRHs, CeRHs, and DmRHs, and one position is also found in RHs from yeast and human. Of the 27 different AtRH structures with introns, 20 have at least one predicted ancient intron in the regions coding for the catalytic domain. In all of the organisms examined, we found at least one gene with most of its intron predicted to be ancient. In A. thaliana, the large diversity in RH structures suggests that duplications of the ancestral RH were followed by a high number of intron deletions and additions. The very high bias toward phase 0 introns is in favor of intron addition, preferentially in phase 0. Results from this comparative study of the same gene family in a plant and in two animals are discussed in terms of the general mechanisms of gene family evolution.

Synchrotron radiation diffraction from two-dimensional protein crystals at the air/water interface

Protein structure determination by classical x-ray crystallography requires three-dimensional crystals that are difficult to obtain for most proteins and especially for membrane proteins. An alternative is to grow two-dimensional (2D) crystals by adsorbing proteins to ligand-lipid monolayers at the surface of water. This confined geometry requires only small amounts of material and offers numerous advantages: self-assembly and ordering over micrometer scales is easier to obtain in two dimensions; although fully hydrated, the crystals are sufficiently rigid to be investigated by various techniques, such as electron crystallography or micromechanical measurements. Here we report structural studies, using grazing incidence synchrotron x-ray diffraction, of three different 2D protein crystals at the air-water interface, namely streptavidine, annexin V, and the transcription factor HupR. Using a set-up of high angular resolution, we observe narrow Bragg reflections showing long-range crystalline order in two dimensions. In the case of streptavidin the angular range of the observed diffraction corresponds to a resolution of 10 A in plane and 14 A normal to the plane. We show that this approach is complementary to electron crystallography but without the need for transfer of the monolayer onto a grid. Moreover, as the 2D crystals are accessible from the buffer solution, the formation and structure of protein complexes can be investigated in situ.

In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants

In the sequences released by the Arabidopsis Genome Initiative (AGI), we discovered a new and unexpectedly large family of orphan genes (127 genes by 01.08.99), named AtPCMP. The distribution of the AtPCMP genes on the five chromosomes suggests that the genome of Arabidopsis thaliana contains more than 200 genes of this family (1% of the whole genome). The deduced AtPCMP proteins are characterized by a surprising combinatorial organization of sequence motifs. The amino-terminal domain is made of a succession of three conserved motifs which generate an important diversity. These proteins are classified into three subfamilies based on the length and nature of their carboxy-terminal domain constituted by 1-6 motifs. All the motifs characterized have an important level of conservation in both sequence and spacing. A specific signature of this large family is defined. The presence of ESTs in databases and the detection of clones in A. thaliana cDNA libraries indicate that most of the genes of this family are expressed. The absence of similar sequences outside the plant kingdom strongly suggests that this unusually large orphan family is unique to plants. Features, the genesis, the potential function and the evolution of this plant combinatorial and modular protein family are discussed.