Multiscale X-ray study of Bacillus subtilis biofilms reveals interlinked structural hierarchy and elemental heterogeneity.

Biofilms are multicellular microbial communities that encase themselves in an extracellular matrix (ECM) of secreted biopolymers and attach to surfaces and interfaces. Bacterial biofilms are detrimental in hospital and industrial settings, but they can be beneficial, for example, in agricultural as well as in food technology contexts. An essential property of biofilms that grants them with increased survival relative to planktonic cells is phenotypic heterogeneity, the division of the biofilm population into functionally distinct subgroups of cells. Phenotypic heterogeneity in biofilms can be traced to the cellular level; however, the molecular structures and elemental distribution across whole biofilms, as well as possible linkages between them, remain unexplored. Mapping X-ray diffraction across intact biofilms in time and space, we revealed the dominant structural features in Bacillus subtilis biofilms, stemming from matrix components, spores, and water. By simultaneously following the X-ray fluorescence signal of biofilms and isolated matrix components, we discovered that the ECM preferentially binds calcium ions over other metal ions, specifically, zinc, manganese, and iron. These ions, remaining free to flow below macroscopic wrinkles that act as water channels, eventually accumulate and may possibly lead to sporulation. The possible link between ECM properties, regulation of metal ion distribution, and sporulation across whole, intact biofilms unravels the importance of molecular-level heterogeneity in shaping biofilm physiology and development.

Multimodal analysis and comparison of stoichiometric and structural characteristics of parosteal and conventional osteosarcoma with massive sclerosis in human bone.

Osteosarcoma (OS) is the most common malignant primary bone tumor in humans and occurs in various subtypes. Tumor formation happens through malignant osteoblasts producing immature bone. In the present paper we studied two different subtypes of osteosarcoma, from one individual with conventional OS with massive sclerosis and one individual with parosteal OS, based on a multimodal approach including small angle x-ray scattering (SAXS), wide angle x-ray diffraction (WAXS), backscattered electron imaging (BEI) and Raman spectroscopy. It was found that both tumors showed reduced mineral particle sizes and degree of orientation of the collagen-mineral composite in the affected areas, alongside with a decreased crystallinity. Distinct differences between the tumor material from the two individuals were found in the degree of mineralization. Further differences were observed in the carbonate to phosphate ratio, which is related to the degree of carbonate substitution in bone mineral and indicative of the turnover rate. The contraction of the c-axis of the bone mineral crystals proved to be a further, very sensitive parameter, potentially indicative of malignancy.

Deflecting Dendrites by Introducing Compressive Stress in Li7La3Zr2O12 Using Ion Implantation.

Lithium dendrites belong to the key challenges of solid-state battery research. They are unavoidable due to the imperfect nature of surfaces containing defects of a critical size that can be filled by lithium until fracturing the solid electrolyte. The penetration of Li metal occurs along the propagating crack until a short circuit takes place. It is hypothesized that ion implantation can be used to introduce stress states into Li6.4La3Zr1.4Ta0.6O12 which enables an effective deflection and arrest of dendrites. The compositional and microstructural changes associated with the implantation of Ag-ions are studied via atom probe tomography, electron microscopy, and nano X-ray diffraction indicating that Ag-ions can be implanted up to 1 µm deep and amorphization takes place down to 650-700 nm, in good agreement with kinetic Monte Carlo simulations. Based on diffraction results pronounced stress states up to -700 MPa are generated in the near-surface region. Such a stress zone and the associated microstructural alterations exhibit the ability to not only deflect mechanically introduced cracks but also dendrites, as demonstrated by nano-indentation and galvanostatic cycling experiments with subsequent electron microscopy observations. These results demonstrate ion implantation as a viable technique to design "dendrite-free" solid-state electrolytes for high-power and energy-dense solid-state batteries.

Mesoscale Confinement in Bagworm Silk: A Hidden Structural Organization.

While silk fibers produced by silkworms and spiders are frequently described as a network of amorphous protein chains reinforced by crystalline ß-sheet nanodomains, the importance of higher-order, self-assembled structures has been recognized for advanced modeling of mechanical properties. General acceptance of hierarchical structural models is, however, currently limited by lack of experimental results. Indeed, X-ray scattering studies of spider's dragline-type fibers have been particularly limited by low crystallinities. Here we are reporting on probing the local structure of exceptionally crystalline bagworm silk fibers by X-ray nanobeam scattering. Probing the comparable thickness of cross sections with an X-ray nanobeam allows removing the strong scattering background from the outer sericin layer and reveals a hidden structural organization due to a radial gradient in diameters of mesoscale nanofibrillar bundles in the fibroin phase. Our results provide direct support for lateral interactions between nanofibrils.

A small-angle X-ray scattering study of red blood cells in continuous flow.

Owing to their large penetration depth and high resolution, X-rays are ideally suited to study structures and structural changes within intact biological cells. For this reason, X-ray-based techniques have been used to investigate adhesive cells on solid supports. However, these techniques cannot easily be transferred to the investigation of suspended cells in flow. Here, an X-ray compatible microfluidic device that serves as a sample delivery system and measurement environment for such studies is presented. As a proof of concept, the microfluidic device is applied to investigate chemically fixed bovine red blood cells by small-angle X-ray scattering (SAXS). A very good agreement is found between in-flow and static SAXS data. Moreover, the data are fitted with a hard-sphere model and screened Coulomb interactions to obtain the radius of the protein hemoglobin within the cells. Thus, the utility of this device for studying suspended cells with SAXS in continuous flow is demonstrated.

Toxicity of eosinophil MBP is repressed by intracellular crystallization and promoted by extracellular aggregation.

Eosinophils are white blood cells that function in innate immunity and participate in the pathogenesis of various inflammatory and neoplastic disorders. Their secretory granules contain four cytotoxic proteins, including the eosinophil major basic protein (MBP-1). How MBP-1 toxicity is controlled within the eosinophil itself and activated upon extracellular release is unknown. Here we show how intragranular MBP-1 nanocrystals restrain toxicity, enabling its safe storage, and characterize them with an X-ray-free electron laser. Following eosinophil activation, MBP-1 toxicity is triggered by granule acidification, followed by extracellular aggregation, which mediates the damage to pathogens and host cells. Larger non-toxic amyloid plaques are also present in tissues of eosinophilic patients in a feedback mechanism that likely limits tissue damage under pathological conditions of MBP-1 oversecretion. Our results suggest that MBP-1 aggregation is important for innate immunity and immunopathology mediated by eosinophils and clarify how its polymorphic self-association pathways regulate toxicity intra- and extracellularly.

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures.

Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses (D1/2) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.

Application of Synchrotron Radiation-Based Micro-Analysis on Cadmium Yellows in Pablo Picasso's Femme.

The cultural heritage community is increasingly exploring synchrotron radiation (SR) based techniques for the study of art and archaeological objects. When considering heterogeneous and complex micro-samples, such as those from paintings, the combination of different SR X-ray techniques is often exploited to overcome the intrinsic limitations and sensitivity of the single technique. Less frequently, SR X-ray analyses are combined with SR micro-photoluminescence or micro-Fourier Transform Infrared spectroscopy, which provide complementary information on the molecular composition, offering a unique integrated analysis approach. Although the spatial correlation between the maps obtained with different techniques is not straightforward due to the different volumes probed by each method, the combination of the information provides a greater understanding and insight into the paint chemistry. In this work, we discuss the advantages and disadvantages of the combination of X-ray techniques and SR-based photoluminescence through the study of two paint micro-samples taken from Pablo Picasso's Femme (1907). The painting contains two cadmium yellow paints (based on CdS): one relatively intact and one visibly degraded. SR micro-analyses demonstrated that the two Cd-yellow paints differ in terms of structure, chemical composition, and photoluminescence properties. In particular, on the basis of the combination of different SR measurements, we hypothesize that the degraded yellow is based on nanocrystalline CdS with high presence of Cd(OH)Cl. These two characteristics have enhanced the reactivity of the paint and strongly influenced its stability.

The "Historical Materials BAG": A New Facilitated Access to Synchrotron X-ray Diffraction Analyses for Cultural Heritage Materials at the European Synchrotron Radiation Facility.

The European Synchrotron Radiation Facility (ESRF) has recently commissioned the new Extremely Brilliant Source (EBS). The gain in brightness as well as the continuous development of beamline instruments boosts the beamline performances, in particular in terms of accelerated data acquisition. This has motivated the development of new access modes as an alternative to standard proposals for access to beamtime, in particular via the "block allocation group" (BAG) mode. Here, we present the recently implemented "historical materials BAG": a community proposal giving to 10 European institutes the opportunity for guaranteed beamtime at two X-ray powder diffraction (XRPD) beamlines-ID13, for 2D high lateral resolution XRPD mapping, and ID22 for high angular resolution XRPD bulk analyses-with a particular focus on applications to cultural heritage. The capabilities offered by these instruments, the specific hardware and software developments to facilitate and speed-up data acquisition and data processing are detailed, and the first results from this new access are illustrated with recent applications to pigments, paintings, ceramics and wood.

Nanobeam X-ray fluorescence and diffraction computed tomography on human bone with a resolution better than 120 nm.

Studying nanostructured hierarchical materials such as the biomineralized bone is challenging due to their complex 3D structures that call for high spatial resolution. One route to study such materials is X-ray powder diffraction computed tomography (XRD-CT) that reveals the 3D distribution of crystalline phases and X-ray fluorescence computed tomography (XRF-CT) that provides element distributions. However, the spatial resolution of XRD-CT has thus far been limited. Here we demonstrate better than 120 nm 3D resolution on human bone in XRD-CT and XRF-CT measured simultaneously using X-ray nanobeams. The results pave the way for nanoscale 3D characterization of nanocrystalline composites like bone at unprecedented detail.

Heterogeneity of the osteocyte lacuno-canalicular network architecture and material characteristics across different tissue types in healing bone.

Various tissue types, including fibrous connective tissue, bone marrow, cartilage, woven and lamellar bone, coexist in healing bone. Similar to most bone tissue type, healing bone contains a lacuno-canalicular network (LCN) housing osteocytes. These cells are known to orchestrate bone remodeling in healthy bone by sensing mechanical strains and translating them into biochemical signals. The structure of the LCN is hypothesized to influence mineralization processes. Hence, the aim of the present study was to visualize and match spatial variations in the LCN topology with mineral characteristics, within and at the interfaces of the different tissue types that comprise healing bone. We applied a correlative multi-method approach to visualize the LCN architecture and quantify mineral particle size and orientation within healing femoral bone in a mouse osteotomy model (26 weeks old C57BL/6 mice). This approach revealed structural differences across several length scales during endochondral ossification within the following regions: calcified cartilage, bony callus, cortical bone and a transition zone between the cortical and callus region analyzed 21 days after the osteotomy. In this transition zone, we observed a continuous convergence of mineral characteristics and osteocyte lacunae shape as well as discontinuities in the lacunae volume and LCN connectivity. The bony callus exhibits a 34% higher lacunae number density and 40% larger lacunar volume compared to cortical bone. The presented correlations between LCN architecture and mineral characteristics improves our understanding of how bone develops during healing and may indicate a contribution of osteocytes to bone (re)modeling.

Large field-of-view scanning small-angle X-ray scattering of mammalian cells.

X-ray imaging is a complementary method to electron and fluorescence microscopy for studying biological cells. In particular, scanning small-angle X-ray scattering provides overview images of whole cells in real space as well as local, high-resolution reciprocal space information, rendering it suitable to investigate subcellular nanostructures in unsliced cells. One persisting challenge in cell studies is achieving high throughput in reasonable times. To this end, a fast scanning mode is used to image hundreds of cells in a single scan. A way of dealing with the vast amount of data thus collected is suggested, including a segmentation procedure and three complementary kinds of analysis, i.e. characterization of the cell population as a whole, of single cells and of different parts of the same cell. The results show that short exposure times, which enable faster scans and reduce radiation damage, still yield information in agreement with longer exposure times.

High-resolution large-area imaging of nanoscale structure and mineralization of a sclerosing osteosarcoma in human bone.

Osteosarcoma is the most common primary bone cancer type in humans. It is predominantly found in young individuals, with a second peak later in life. The tumour is formed by malignant osteoblasts and consists of collagenous, sometimes also mineralized, bone matrix. While the morphology of osteosarcoma has been well studied, there is virtually no information about the nanostructure of the tumour and changes in mineralization on the nanoscale level. In the present paper, human bone tissue inside, next to and remote from a sclerosing osteosarcoma was studied with small angle x-ray scattering, x-ray diffraction and electron microscopy. Quantitative evaluation of nanostructure parameters was combined with high resolution, large area mapping to obtain microscopic images with nanostructure parameter contrast. It was found that the tumour regions were characterized by a notable reduction in mineral particle size, while the mineral content was even higher than that in normal bone. Furthermore, the normal preferential orientation of mineral particles along the longitudinal direction of corticalis or trabeculae was largely suppressed. Also the bone mineral crystal structure was affected: severe crystal lattice distortions were detected in mineralized tumour tissue pointing to a different ion substitution of hydroxyl apatite in tumorous tissue than in healthy tissue.

Diamond nanofocusing refractive X-ray lenses made by planar etching technology.

The manufacturing steps and first tests of a refractive lens made of polycrystalline diamond are described. A fabrication process based on electron-beam lithography and deep reactive ion etching is introduced. Experimental tests on beamline ID13 at the ESRF have been performed. A spot size of 360 nm (FWHM) at an energy E = 24.3 keV is observed.

Fate of MgSiO3 melts at core-mantle boundary conditions.

One key for understanding the stratification in the deep mantle lies in the determination of the density and structure of matter at high pressures, as well as the density contrast between solid and liquid silicate phases. Indeed, the density contrast is the main control on the entrainment or settlement of matter and is of fundamental importance for understanding the past and present dynamic behavior of the deepest part of the Earth's mantle. Here, we adapted the X-ray absorption method to the small dimensions of the diamond anvil cell, enabling density measurements of amorphous materials to unprecedented conditions of pressure. Our density data for MgSiO3 glass up to 127 GPa are considerably higher than those previously derived from Brillouin spectroscopy but validate recent ab initio molecular dynamics simulations. A fourth-order Birch-Murnaghan equation of state reproduces our experimental data over the entire pressure regime of the mantle. At the core-mantle boundary (CMB) pressure, the density of MgSiO3 glass is 5.48 ± 0.18 g/cm(3), which is only 1.6% lower than that of MgSiO3 bridgmanite at 5.57 g/cm(3), i.e., they are the same within the uncertainty. Taking into account the partitioning of iron into the melt, we conclude that melts are denser than the surrounding solid phases in the lowermost mantle and that melts will be trapped above the CMB.

Myelin structure in unfixed, single nerve fibers: Scanning X-ray microdiffraction with a beam size of 200nm.

Previous raster-scanning with a 1µm X-ray beam of individual, myelinated fibers from glutaraldehyde-fixed rat sciatic nerve revealed a spatially-dependent variation in the diffraction patterns from single fibers. Analysis indicated differences in the myelin periodicity, membrane separations, distribution of proteins, and orientation of membrane lamellae. As chemical fixation is known to produce structural artifacts, we sought to determine in the current study whether the structural heterogeneity is intrinsic to unfixed myelin. Using a 200nm-beam that was about five-fold smaller than before, we raster-scanned individual myelinated fibers from both the peripheral (PNS; mouse and rat sciatic nerves) and central (CNS; rat corpus callosum) nervous systems. As expected, the membrane stacking in the internodal region was nearly parallel to the fiber axis and in the paranodal region it was perpendicular to the axis. A myelin lattice was also frequently observed when the incident beam was injected en face to the sheath. Myelin periodicity and diffracted intensity varied with axial position along the fiber, as did the calculated membrane profiles. Raster-scanning with an X-ray beam at sub-micron resolution revealed for the first time that the individual myelin sheaths in unfixed nerve are heterogeneous in both membrane structure and packing.

Scanning X-ray diffraction on cardiac tissue: automatized data analysis and processing.

A scanning X-ray diffraction study of cardiac tissue has been performed, covering the entire cross section of a mouse heart slice. To this end, moderate focusing by compound refractive lenses to micrometer spot size, continuous scanning, data acquisition by a fast single-photon-counting pixel detector, and fully automated analysis scripts have been combined. It was shown that a surprising amount of structural data can be harvested from such a scan, evaluating the local scattering intensity, interfilament spacing of the muscle tissue, the filament orientation, and the degree of anisotropy. The workflow of data analysis is described and a data analysis toolbox with example data for general use is provided. Since many cardiomyopathies rely on the structural integrity of the sarcomere, the contractile unit of cardiac muscle cells, the present study can be easily extended to characterize tissue from a diseased heart.

Point focusing with flat and wedged crossed multilayer Laue lenses.

Point focusing measurements using pairs of directly bonded crossed multilayer Laue lenses (MLLs) are reported. Several flat and wedged MLLs have been fabricated out of a single deposition and assembled to realise point focusing devices. The wedged lenses have been manufactured by adding a stress layer onto flat lenses. Subsequent bending of the structure changes the relative orientation of the layer interfaces towards the stress-wedged geometry. The characterization at ESRF beamline ID13 at a photon energy of 10.5 keV demonstrated a nearly diffraction-limited focusing to a clean spot of 43 nm × 44 nm without significant side lobes with two wedged crossed MLLs using an illuminated aperture of approximately 17 µm × 17 µm to eliminate aberrations originating from layer placement errors in the full 52.7 µm × 52.7 µm aperture. These MLLs have an average individual diffraction efficiency of 44.5%. Scanning transmission X-ray microscopy measurements with convenient working distances were performed to demonstrate that the lenses are suitable for user experiments. Also discussed are the diffraction and focusing properties of crossed flat lenses made from the same deposition, which have been used as a reference. Here a focal spot size of 28 nm × 33 nm was achieved and significant side lobes were noticed at an illuminated aperture of approximately 23 µm × 23 µm.

SiO_{2} Glass Density to Lower-Mantle Pressures.

The convection or settling of matter in the deep Earth's interior is mostly constrained by density variations between the different reservoirs. Knowledge of the density contrast between solid and molten silicates is thus of prime importance to understand and model the dynamic behavior of the past and present Earth. SiO_{2} is the main constituent of Earth's mantle and is the reference model system for the behavior of silicate melts at high pressure. Here, we apply our recently developed x-ray absorption technique to the density of SiO_{2} glass up to 110 GPa, doubling the pressure range for such measurements. Our density data validate recent molecular dynamics simulations and are in good agreement with previous experimental studies conducted at lower pressure. Silica glass rapidly densifies up to 40 GPa, but the density trend then flattens to become asymptotic to the density of SiO_{2} minerals above 60 GPa. The density data present two discontinuities at ∼17 and ∼60 GPa that can be related to a silicon coordination increase from 4 to a mixed 5/6 coordination and from 5/6 to sixfold, respectively. SiO_{2} glass becomes denser than MgSiO_{3} glass at ∼40 GPa, and its density becomes identical to that of MgSiO_{3} glass above 80 GPa. Our results on SiO_{2} glass may suggest that a variation of SiO_{2} content in a basaltic or pyrolitic melt with pressure has at most a minor effect on the final melt density, and iron partitioning between the melts and residual solids is the predominant factor that controls melt buoyancy in the lowermost mantle.

Rapid Acquisition of X-Ray Scattering Data from Droplet-Encapsulated Protein Systems.

Encapsulating reacting biological or chemical samples in microfluidic droplets has the great advantage over single-phase flows of providing separate reaction compartments. These compartments can be filled in a combinatoric way and prevent the sample from adsorbing to the channel walls. In recent years, small-angle X-ray scattering (SAXS) in combination with microfluidics has evolved as a nanoscale method of such systems. Here, we approach two major challenges associated with combining droplet microfluidics and SAXS. First, we present a simple, versatile, and reliable device, which is both suitable for stable droplet formation and compatible with in situ X-ray measurements. Second, we solve the problem of "diluting" the sample signal by the signal from the oil separating the emulsion droplets by multiple fast acquisitions per droplet and data thresholding. We show that using our method, even the weakly scattering protein vimentin provides high signal-to-noise ratio data.