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.

Pulse picker for synchrotron radiation driven by a surface acoustic wave: erratum.

An erratum is presented to correct the typographical errors concerning the composition of the multilayer used in the experiment in Opt. Lett. 42, 1915.

Carbon-based Fresnel optics for hard x-ray astronomy.

We investigate the potential of large-scale diffractive-refractive normal-incidence transmission lenses for the development of space-based hard x-ray telescopes with an angular resolution in the range of (10-6-10-3) arcsec over a field of view that is restricted by the available detector size. Coherently stepped achromatic lenses with diameters up to 5 m for compact apertures and 13 m in the case of segmentation provide an access to spectrally resolved imaging within keV-wide bands around the design energy between 10 and 30 keV. Within an integration time of 106 s, a photon-limited 5σ sensitivity down to (10-9-10-7) s-1 cm-2 keV-1 can be achieved depending on the specific design. An appropriate fabrication strategy, feasible nowadays with micro-optical technologies, is considered and relies on the availability of high-purity carbon or polymer membranes. X-ray fluorescence measurements of various commercially available carbon-based materials prove for most of them the existence of a virtually negligible contamination by critical trace elements such as transition metals on the ppm level.

Pulse picker for synchrotron radiation driven by a surface acoustic wave.

A functional test for a pulse picker for synchrotron radiation was performed at Diamond Light Source. The purpose of a pulse picker is to select which pulse from the synchrotron hybrid-mode bunch pattern reaches the experiment. In the present work, the Bragg reflection on a Si/B4C multilayer was modified using surface acoustic wave (SAW) trains. Diffraction on the SAW alters the direction of the x rays and it can be used to modulate the intensity of the x rays that reach the experimental chamber. Using electronic modulation of the SAW amplitude, it is possible to obtain different scattering conditions for different x-ray pulses. To isolate the single bunch, the state of the SAW must be changed in the short time gap between the pulses. To achieve the necessary time resolution, the measurements have been performed in conical diffraction geometry. The achieved time resolution was 120 ns.

Giant pressure-induced volume collapse in the pyrite mineral MnS2.

Dramatic volume collapses under pressure are fundamental to geochemistry and of increasing importance to fields as diverse as hydrogen storage and high-temperature superconductivity. In transition metal materials, collapses are usually driven by so-called spin-state transitions, the interplay between the single-ion crystal field and the size of the magnetic moment. Here we show that the classical S = 5/2 mineral hauerite (MnS2) undergoes an unprecedented (ΔV ~ 22%) collapse driven by a conceptually different magnetic mechanism. Using synchrotron X-ray diffraction we show that cold compression induces the formation of a disordered intermediate. However, using an evolutionary algorithm we predict a new structure with edge-sharing chains. This is confirmed as the thermodynamic ground state using in situ laser heating. We show that magnetism is globally absent in the new phase, as low-spin quantum S = 1/2 moments are quenched by dimerization. Our results show how the emergence of metal-metal bonding can stabilize giant spin-lattice coupling in Earth's minerals.

Exceptional adsorption-induced cluster and network deformation in the flexible metal-organic framework DUT-8(Ni) observed by in situ X-ray diffraction and EXAFS.

The "gate opening" mechanism in the highly flexible MOF Ni2(2,6-ndc)2dabco (DUT-8(Ni), DUT = Dresden University of Technology) with unprecedented unit cell volume change was elucidated in detail using combined single crystal X-ray diffraction, in situ XRD and EXAFS techniques. The analysis of the crystal structures of closed pore (cp) and large pore (lp) phases reveals a drastic and unique unit cell volume expansion of up to 254%, caused by adsorption of gases, surpassing other gas-pressure switchable MOFs significantly. To a certain extent, the structural deformation is specific for the guest molecule triggering the transformation due to subtle differences in adsorption enthalpy, shape, and kinetic diameter of the guest. Combined adsorption and powder diffraction experiments using nitrogen (77 K), carbon dioxide (195 K), and n-butane (272.5 K) as a probe molecules reveal a one-step structural transformation from cp to lp. In contrast, adsorption of ethane (185 K) or ethylene (169 K) results in a two-step transformation with the formation of intermediate phases. In situ EXAFS during nitrogen adsorption was used for the first time to monitor the local coordination geometry of the metal atoms during the structural transformation in flexible MOFs revealing a unique local deformation of the nickel-based paddle-wheel node.

In situ observation of gating phenomena in the flexible porous coordination polymer Zn2(BPnDC)2(bpy) (SNU-9) in a combined diffraction and gas adsorption experiment.

The intrinsic structural dynamic during the adsorption of CO2 at 195 K and N2 at 77 K on flexible porous coordination polymer Zn2(BPnDC)2(bpy) (SNU-9) was studied in situ by powder XRD. The crystal structures of as made and solvent free (activated) phases were determined by single crystal X-ray diffraction. During the structural transformation caused by activation, the rearrangement of Zn-O bonds occurs that leads to changes in coordination environment of Zn atoms. Such changes lead to the contraction of the unit cell and to decreasing unit cell volume of nearly 28% in comparison to the pristine as made structure. The solvent accessible volume of the unit cell decreases from 40.8% to 12.8%. The adsorption of CO2 and N2 on SNU-9 proceeds in a different way: the formation of intermediate phase during the CO2 adsorption could be postulated, while the transformation from narrow pore form to the open structure occurs in quasi-one-step in the case of N2 adsorption (the intermediate phase is formed only in very narrow pressure region). The transformation of the structure is guest dependent and the differences in the structures of CO2@SNU-9 at 195 K and N2@SNU-9 at 77 K were proven by Pawley and Rietveld refinements of powder XRD patterns. The structure of N2@SNU-9 is identical to this of as synthesized phase, while the structure of CO2@SNU-9 differs slightly.

Conformation-controlled sorption properties and breathing of the aliphatic Al-MOF [Al(OH)(CDC)].

The Al-MOF CAU-13 ([Al(OH)(trans-CDC)]; trans-H2CDC = trans-1,4-cyclohexanedicarboxylic acid) is structurally related to the MIL-53 compounds that are well-known for their "breathing" behavior, i.e., the framework flexibility upon external stimuli such as the presence of adsorbate molecules. The adsorption properties of CAU-13 were investigated in detail. The sorption isotherms of N2, H2, CH4, CO, CO2, and water were recorded, and the adsorption enthalpies for the gases were determined by microcalorimetry. The structural changes upon adsorption of CO2 were followed with in situ synchrotron powder X-ray diffraction (PXRD). The patterns were analyzed by parametric unit cell refinement, and the preferential arrangement of the CO2 molecules was modeled by density functional theory calculations. The adsorption and separation of mixtures of o-, m-, and p-xylene from mesitylene showed a preferred adsorption of o-xylene. The structures of o/m/p-xylene-loaded CAU-13 were determined from PXRD data. The adsorption of xylene isomers induces a larger pore opening than that in the thermal activation of CAU-13. In the crystal structure of the activated sample CAU-13(empty pore), half of the linkers adopt the a,a confirmation and the other half the e,e conformation, and the presence of a,a-CDC(2-) ions hampers the structural flexibility of CAU-13. However, after the adsorption of xylene, all linkers are present in the e,e conformation, allowing for a wider pore opening by this new type of "breathing".

Direct observation of liquid pre-crystallization intermediates during the reduction of aqueous tetrachloroaurate by sulfide ions.

Phenomena preceding precipitation of gold(i) sulfide in the reaction of aqueous tetrachloroauric acid with sodium sulfide have been studied applying several time-resolved in situ techniques. As can be deduced from UV-vis absorption spectroscopy, soluble species ("pre-nucleation clusters") emerge within several seconds and slightly change with time; the spectra, along with the previous data for the immobilized products, are indicative of disordered matter with Au(I)-S bonding and the gap of about 1.5 eV. In situ tapping-mode atomic force microscopy (AFM) directly imaged "soft" droplet-like species from 20-50 nm to about 200 nm in the lateral size and the continuous film condensed on the highly oriented pyrolytic graphite (HOPG) support. Small-angle X-ray scattering (SAXS) revealed quasi-particles ("liquid clusters") growing to about 12 nm for 30 min, and slowly afterwards. Dynamic light scattering (DLS) was preferentially due to the larger species, although the liquid clusters within 20 nm comprise more than 80% of the total volume of the fluid products. The entities, which exist in solution for many hours before sudden gold sulfide sedimentation, are considered as "dense liquid" intermediates involved in a non-classical nucleation pathway.

Nanocrystal residual strains and density layers enhance failure resistance in the cleithrum bone of evolutionary advanced pike fish.

Failure-resistant designs are particularly crucial for bones subjected to rapid loading, as is the case for the ambush-hunting northern pike (Esox lucius). These fish have slim and low-density osteocyte-lacking bones. As part of the swallowing mechanism, the cleithrum bone opens and closes the jaw. The cleithrum needs sufficient strength and damage tolerance, to withstand years of repetitive rapid gape-and-suck cycles of feeding. The thin wing-shaped bone comprises anisotropic layers of mineralized collagen fibers that exhibit periodic variations in mineral density on the mm and micrometer length scales. Wavy collagen fibrils interconnect these layers yielding a highly anisotropic structure. Hydrated cleithra exhibit Young's moduli spanning 3-9 GPa where the yield stress of ∼40 MPa increases markedly to exceed ∼180 MPa upon drying. This 5x observation of increased strength corresponds to a change to brittle fracture patterns. It matches the emergence of compressive residual strains of ∼0.15% within the mineral crystals due to forces from shrinking collagen layers. Compressive stresses on the nanoscale, combined with the layered anisotropic microstructure on the mm length scale, jointly confer structural stability in the slender and lightweight bones. By employing a range of X-ray, electron and optical imaging and mechanical characterization techniques, we reveal the structure and properties that make the cleithra impressively damage resistant composites. STATEMENT OF SIGNIFICANCE: By combining structural and mechanical characterization techniques spanning the mm to the sub-nanometer length scales, this work provides insights into the structural organization and properties of a resilient bone found in pike fish. Our observations show how the anosteocytic bone within the pectoral gridle of these fish, lacking any biological (remodeling) repair mechanisms, is adapted to sustain natural repeated loading cycles of abrupt jaw-gaping and swallowing. We find residual strains within the mineral apatite nanocrystals that contribute to forming a remarkably resilient composite material. Such information gleaned from bony structures that are different from the usual bones of mammals showcases how nature incorporates smart features that induce damage tolerance in bone material, an adaptation acquired through natural evolutionary processes.

In situ cell for grazing-incidence x-ray diffraction on thin films in thermal catalysis.

A cell for synchrotron-based grazing-incidence x-ray diffraction at ambient pressures and moderate temperatures in a controlled gas atmosphere is presented. The cell is suited for the in situ study of thin film samples under catalytically relevant conditions. To some extent, in addition to diffraction, the cell can be simultaneously applied for x-ray reflectometry and fluorescence studies. Different domes enclosing the sample have been studied and selected to ensure minimum contribution to the diffraction patterns. The applicability of the cell is demonstrated using synchrotron radiation by monitoring structural changes of a 3 nm Pd thin film upon interaction with gas-phase hydrogen and during acetylene semihydrogenation at 150 °C. The cell allows investigation of very thin films under catalytically relevant conditions.

Acidic Osteoid Templates the Plywood Structure of Bone Tissue.

Bone is created by osteoblasts that secrete osteoid after which an ordered texture emerges, followed by mineralization. Plywood geometries are a hallmark of many trabecular and cortical bones, yet the origin of this texturing in vivo has never been shown. Nevertheless, extensive in vitro work revealed how plywood textures of fibrils can emerge from acidic molecular cholesteric collagen mesophases. This study demonstrates in sheep, which is the preferred model for skeletal orthopaedic research, that the deeper non-fibrillar osteoid is organized in a liquid-crystal cholesteric geometry. This basophilic domain, rich in acidic glycosaminoglycans, exhibits low pH which presumably fosters mesoscale collagen molecule ordering in vivo. The results suggest that the collagen fibril motif of twisted plywood matures slowly through self-assembly thermodynamically driven processes as proposed by the Bouligand theory of biological analogues of liquid crystals. Understanding the steps of collagen patterning in osteoid-maturation processes may shed new light on bone pathologies that emerge from collagen physico-chemical maturation imbalances.

Primary radiation damage in bone evolves via collagen destruction by photoelectrons and secondary emission self-absorption.

X-rays are invaluable for imaging and sterilization of bones, yet the resulting ionization and primary radiation damage mechanisms are poorly understood. Here we monitor in-situ collagen backbone degradation in dry bones using second-harmonic-generation and X-ray diffraction. Collagen breaks down by cascades of photon-electron excitations, enhanced by the presence of mineral nanoparticles. We observe protein disintegration with increasing exposure, detected as residual strain relaxation in pre-stressed apatite nanocrystals. Damage rapidly grows from the onset of irradiation, suggesting that there is no minimal 'safe' dose that bone collagen can sustain. Ionization of calcium and phosphorous in the nanocrystals yields fluorescence and high energy electrons giving rise to structural damage that spreads beyond regions directly illuminated by the incident radiation. Our findings highlight photoelectrons as major agents of damage to bone collagen with implications to all situations where bones are irradiated by hard X-rays and in particular for small-beam mineralized collagen fiber investigations.

Clay pigment structure characterisation as a guide for provenance determination--a comparison between laboratory powder micro-XRD and synchrotron radiation XRD.

Application of X-ray diffraction (XRD)-based techniques in the analysis of painted artworks is not only beneficial for indisputable identification of crystal constituents in colour layers, but it can also bring insight in material crystal structure, which can be affected by their geological formation, manufacturing procedure or secondary changes. This knowledge might be helpful for art historic evaluation of an artwork as well as for its conservation. By way of example of kaolinite, we show that classification of its crystal structure order based on XRD data is useful for estimation of its provenance. We found kaolinite in the preparation layer of a Gothic wall painting in a Czech church situated near Karlovy Vary, where there are important kaolin deposits. Comparing reference kaolin materials from eight various Czech deposits, we found that these can be differentiated just according to the kaolinite crystallinity. Within this study, we compared laboratory powder X-ray micro-diffraction (micro-XRD) with synchrotron radiation X-ray diffraction analysing the same real sample. We found that both techniques led to the same results.

Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple-edge anomalous diffraction.

Multiple-Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order-disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X-ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f' and f'' of the energy of the radiation, especially close to the element-specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC-2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X-ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz-kesterite structure type.

Observation of sagittal X-ray diffraction by surface acoustic waves in Bragg geometry.

X-ray Bragg diffraction in sagittal geometry on a Y-cut langasite crystal (La3Ga5SiO14) modulated by Λ = 3 µm Rayleigh surface acoustic waves was studied at the BESSY II synchrotron radiation facility. Owing to the crystal lattice modulation by the surface acoustic wave diffraction, satellites appear. Their intensity and angular separation depend on the amplitude and wavelength of the ultrasonic superlattice. Experimental results are compared with the corresponding theoretical model that exploits the kinematical diffraction theory. This experiment shows that the propagation of the surface acoustic waves creates a dynamical diffraction grating on the crystal surface, and this can be used for space-time modulation of an X-ray beam.

Scaffold curvature-mediated novel biomineralization process originates a continuous soft tissue-to-bone interface.

A myriad of shapes are found in biological tissues, often naturally evolved to fulfill a particular function. In the field of tissue engineering, substrate geometry influences cell behavior and tissue formation in vitro, yet little is known how this translates to an in vivo scenario. Here we investigate scaffold curvature-induced tissue growth, without additional growth factors or cells, in an ovine animal model. We show that soft tissue formation follows a curvature-driven tissue growth model. The highly organized endogenous soft matrix, potentially under mechanical strain, leads to a non-standard form of biomineralization, whereby the pre-existing organic matrix is mineralized without collagen remodeling and without an intermediate cartilage ossification phase. Micro- and nanoscale characterization of the tissue microstructure using histology, backscattered electron (BSE) and second-harmonic generation (SHG) imaging and synchrotron small angle X-ray scattering (SAXS) revealed (i) continuous collagen fibers across the soft-hard tissue interface on the tip of mineralized cones, and (ii) bone remodeling by basic multicellular units (BMUs) in regions adjacent to the native cortical bone. Thus, features of soft tissue-to-bone interface resembling the insertion sites of ligaments and tendons into bone were created, using a scaffold that did not mimic the structural or biological gradients across such a complex interface at its mature state. This study provides fundamental knowledge for biomimetic scaffold design in the fields of bone regeneration and soft tissue-to-bone interface tissue engineering. STATEMENT OF SIGNIFICANCE: Geometry influences cell behavior and tissue formation in vitro. However, little is known how this translates to an in vivo scenario. Here we investigate the influence of scaffold mean surface curvature on in vivo tissue growth using an ovine animal model. Based on a multiscale tissue microstructure characterization, we show a seamless integration of soft tissue into newly formed bone, resembling the insertion sites of ligaments and tendons into bone. This interface was created using a scaffold without additional growth factors or cells that did not recapitulate the structural or biological gradients across such a complex tissue interface at its mature state. These findings have important implications for biomimetic scaffold design for bone regeneration and soft tissue-to-bone interface tissue engineering.

A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the new DPDAK package to small-angle X-ray scattering and grazing-incidence small-angle X-ray scattering.

X-ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open-source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one- or two-dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software, DPDAK (directly programmable data analysis kit), is based on a plug-in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use of DPDAK for on- and offline analysis of scanning small-angle X-ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing-incidence SAXS data. In addition to a comparison with existing software packages, the structure of DPDAK and the possibilities and limitations are discussed.

The influence of electrical stimulation of vagus nerve on elemental composition of dopamine related brain structures in rats.

Recent studies of Parkinson's disease indicate that dorsal motor nucleus of nerve vagus is one of the earliest brain areas affected by alpha-synuclein and Lewy bodies pathology. The influence of electrical stimulation of vagus nerve on elemental composition of dopamine related brain structures in rats is investigated. Synchrotron radiation based X-ray fluorescence was applied to the elemental micro-imaging and quantification in thin tissue sections. It was found that elements such as P, S, Cl, K, Ca, Fe, Cu, Zn, Se, Br and Rb are present in motor cortex, corpus striatum, nucleus accumbens, substantia nigra, ventral tectal area, and dorsal motor nucleus of vagus. The topographic analysis shows that macro-elements like P, S, Cl and K are highly concentrated within the fiber bundles of corpus striatum. In contrast the levels of trace elements like Fe and Zn are the lowest in these structures. It was found that statistically significant differences between the animals with electrical stimulation of vagus nerve and the control are observed in the left side of corpus striatum for P (p = 0.04), S (p = 0.02), Cl (p = 0.05), K (p = 0.02), Fe (p = 0.04) and Zn (p = 0.02). The mass fractions of these elements are increased in the group for which the electrical stimulation of vagus nerve was performed. Moreover, the contents of Ca (p = 0.02), Zn (p = 0.07) and Rb (p = 0.04) in substantia nigra of right hemisphere are found to be significantly lower in the group with stimulation of vagus nerve than in the control rats.

Combining scanning probe microscopy and x-ray spectroscopy.

A new versatile tool, combining Shear Force Microscopy and X-Ray Spectroscopy was designed and constructed to obtain simultaneously surface topography and chemical mapping. Using a sharp optical fiber as microscope probe, it is possible to collect locally the visible luminescence of the sample. Results of tests on ZnO and on ZnWO4 thin layers are in perfect agreement with that obtained with other conventional techniques. Twin images obtained by simultaneous acquisition in near field of surface topography and of local visible light emitted by the sample under X-Ray irradiation in synchrotron environment are shown. Replacing the optical fibre by an X-ray capillary, it is possible to collect local X-ray fluorescence of the sample. Preliminary results on Co-Ti sample analysis are presented.