Location, speciation, and quantification of carbon in silica phytoliths using synchrotron scanning transmission X-ray microspectroscopy.

Phytoliths of biogenic silica play a vital role in the silicon biogeochemical cycle and occlude a fraction of organic carbon. The location, chemical speciation, and quantification of this carbon within phytoliths have remained elusive due to limited direct experimental evidence. In this work, phytoliths (bilobate morphotype) from the sugarcane stalk epidermis are sectioned with a focused ion beam to produce lamellas (≈10 × 10 µm2 size, <500 nm thickness) and probed by synchrotron scanning transmission X-ray microspectroscopy (≈100-200 nm pixel size; energies near the silicon and carbon K-absorption edges). Analysis of the spectral image stacks reveals the complementarity of the silica and carbon spatial distributions, with carbon found at the borders of the lamellas, in islands within the silica, and dispersed in extended regions that can be described as a mixed silica-carbonaceous matrix. Carbon spectra are assigned mainly to lignin-like compounds as well as to proteins. Carbon contents of 3-14 wt.% are estimated from the spectral maps of four distinct phytolith lamellas. The results provide unprecedented spatial and chemical information on the carbon in phytoliths obtained without interference from wet-chemical digestion.

In vitro assessment of internal implant-abutment connections with different cone angles under static loading using synchrotron-based radiation.

BACKGROUND: The stability of implant-abutment connection is crucial to minimize mechanical and biological complications. Therefore, an assessment of the microgap behavior and abutment displacement in different implant-abutment designs was performed. METHODS: Four implant systems were tested, three with a conical implant-abutment connection based on friction fit and a cone angle < 12 ° (Medentika, Medentis, NobelActive) and a system with an angulated connection (< 40°) (Semados). In different static loading conditions (30 N - 90º, 100 N - 90º, 200 N - 30º) the microgap and abutment displacement was evaluated using synchrotron-based microtomography and phase-contrast radioscopy with numerical forward simulation of the optical Fresnel propagation yielding an accuracy down to 0.1 µm. RESULTS: Microgaps were present in all implant systems prior to loading (0.15-9 µm). Values increased with mounting force and angle up to 40.5 µm at an off axis loading of 100 N in a 90° angle. CONCLUSIONS: In contrast to the implant-abutment connection with a large cone angle (45°), the conical connections based on a friction fit (small cone angles with < 12°) demonstrated an abutment displacement which resulted in a deformation of the outer implant wall. The design of the implant-abutment connection seems to be crucial for the force distribution on the implant wall which might influence peri-implant bone stability.

Efficient in situ screening of and data collection from microcrystals in crystallization plates.

A considerable bottleneck in serial crystallography at XFEL and synchrotron sources is the efficient production of large quantities of homogenous, well diffracting microcrystals. Efficient high-throughput screening of batch-grown microcrystals and the determination of ground-state structures from different conditions is thus of considerable value in the early stages of a project. Here, a highly sample-efficient methodology to measure serial crystallography data from microcrystals by raster scanning within standard in situ 96-well crystallization plates is described. Structures were determined from very small quantities of microcrystal suspension and the results were compared with those from other sample-delivery methods. The analysis of a two-dimensional batch crystallization screen using this method is also described as a useful guide for further optimization and the selection of appropriate conditions for scaling up microcrystallization.

Adaptable SEC-SAXS data collection for higher quality structure analysis in solution.

The two major challenges in synchrotron size-exclusion chromatography coupled in-line with small-angle x-ray scattering (SEC-SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation-damaged materials on the walls of the sample cell. In recent years, many post-experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC-SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4-2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4-2). The first mode, the High-Resolution mode, enables SEC-SAXS data collection with excellent sample separation and virtually no additional peak broadening from the UHPLC UV detector to the x-ray position by taking advantage of the low system dispersion of the UHPLC. The small bed volume of the analytical SEC column minimizes sample dilution in the column and facilitates data collection at higher sample concentrations with excellent sample economy equal to or even less than that of the conventional equilibrium SAXS method. Radiation damage problems during SEC-SAXS data collection are evaded by additional cleaning of the sample cell after buffer data collection and avoidance of unnecessary exposures through the use of the x-ray shutter control options, allowing sample data collection with a clean sample cell. Therefore, accurate background subtraction can be performed at a level equivalent to the conventional equilibrium SAXS method without requiring baseline correction, thereby leading to more reliable downstream structural analysis and quicker access to new science. The two other data collection modes, the High-Throughput mode and the Co-Flow mode, add agility to the planning and execution of experiments to efficiently achieve the user's scientific objectives at the SSRL BL4-2.

Crystallization and In Situ Room Temperature Data Collection Using the Crystallization Facility at Harwell and Beamline VMXi, Diamond Light Source.

Protocols for robotic protein crystallization using the Crystallization Facility at Harwell and in situ room temperature data collection from crystallization plates at Diamond Light Source beamline VMXi are described. This approach enables high-quality room-temperature crystal structures to be determined from multiple crystals in a straightforward manner and provides very rapid feedback on the results of crystallization trials as well as enabling serial crystallography. The value of room temperature structures in understanding protein structure, ligand binding, and dynamics is becoming increasingly recognized in the structural biology community. This pipeline is accessible to users from all over the world with several available modes of access. Crystallization experiments that are set up can be imaged and viewed remotely with crystals identified automatically using a machine learning tool. Data are measured in a queue-based system with up to 60° rotation datasets from user-selected crystals in a plate. Data from all the crystals within a particular well or sample group are automatically merged using xia2.multiplex with the outputs straightforwardly accessed via a web browser interface.

Characterizing the microstructures of mammalian enamel by synchrotron phase contrast microCT.

The enamel of mammalian teeth is a highly mineralized tissue that must endure a lifetime of cyclic contact and is inspiring the development of next-generation engineering materials. Attempts to implement enamel-inspired structures in synthetic materials have had limited success, largely due to the absence of a detailed understanding of its microstructure. The present work used synchrotron phase-contrast microCT imaging to evaluate the three-dimensional microstructure of enamel from four mammals including Lion, Gray Wolf, Snow Leopard, and Black Bear. Quantitative results of image analysis revealed that the decussation pattern of enamel consists of discrete diazone (D) and parazone (P) bands of rods organized with stacking arrangement of D+/P/D-/P in all mammals evaluated; the D+ and D- refer to distinct diazone bands with juxtaposed rod orientations from the reference plane. Furthermore, the rod orientations in the bands can be described in terms of two principal angles, defined here as the pitch and yaw. While the pitch angle increases from the outer enamel to a maximum (up to ≈ 40°) near the dentin enamel junction, minimal spatial variations are observed in yaw across the enamel thickness. There are clear differences in the decussation parameters of enamel across species that are interpreted here with respect to the structural demands placed on their teeth. The rod pitch and band width of enamel are identified as important design parameters and appear to be correlated with the bite force quotient of the four mammals evaluated. STATEMENT OF SIGNIFICANCE: The multi-functionality of tooth enamel requires both hardness and resistance to fracture, properties that are generally mutually exclusive. Ubiquitous to all mammalian teeth, the enamel is expected to have undergone adaptations in microstructure to accommodate the differences in diet, body size and bite force across animals. For the first time, we compare the complex three-dimensional microstructure of enamel from teeth of multiple mammalian species using synchrotron micro-computed tomography. The findings provide new understanding of the "design" of mammalian enamel microstructures, as well as how specific parameters associated with the decussation of rods appear to be engineered to modulate its fracture resistance.

High-Throughput Interactome Determination via Sulfur Anomalous Scattering.

We propose a novel approach for detecting the binding between proteins making use of the anomalous diffraction of natively present heavy elements, e.g., sulfurs, inside molecular three-dimensional structures. In particular, we analytically and numerically show that the diffraction patterns produced by the anomalous scattering of the sulfur atoms in a given direction depend additively on the relative distances between all couples of sulfur atoms. Thus, the differences in the patterns produced by bound proteins with respect to their nonbonded states can be exploited to rapidly assess protein complex formation. On the basis of our results, we suggest a possible experimental procedure for detecting protein-protein binding. Overall, the completely label-free and rapid method we propose may be readily extended to probe interactions on a large scale, thus paving the way for the development of a novel field of research based on a synchrotron light source.

Mechanistic analysis of the sub chronic toxicity of La and Gd in Daphnia magna based on TKTD modelling and synchrotron X-ray fluorescence imaging.

The release of lanthanides (Ln) into the environment has increased in recent decades due to their expanding applications in society. Studying their toxicity in aquatic ecosystems is urgent and challenging, with contradictory evidence presented in the literature. This study compared the biodistribution of La and Gd in Daphnia magna exposed to sub-chronic conditions and developed the first Toxicokinetic-Toxicodynamic (TKTD) model for these lanthanides with this model crustacean. D. magna were initially exposed for 7 days to concentrations close to the LC50 of La (2.10 mg L-1) and Gd (1.70 mg L-1). After exposure, half of the live daphnids were introduced in a clean media to allow depuration over 24 h, while the other organisms were directly prepared for synchrotron imaging measurements. Synchrotron X-ray fluorescence analysis revealed that metal distribution in the organisms was similar for both La and Gd, predominantly localized in the intestinal tract, even after the depuration process. These results indicate that ingested metal can adversely affect organisms under sub-chronic exposure conditions, highlighting the importance of using nominal concentrations as a more suitable indicator of metal bioavailability for risk assessment. The General Unified Threshold Model of Survival (GUTS) TKTD framework, in its reduced form (GUTS-RED), was developed for La and Gd using dissolved and nominal concentrations. D. magna were exposed for 7 days to concentrations from 0.5 to 5 mg L-1 of La or Gd and mortality monitored daily. The mechanistic model revealed a faster toxicokinetics for La than Gd and a higher toxicity for Gd than La in the organism. This study confirmed, despite similar chemical properties, the variation in both toxicity and toxicokinetics between these two metals.

Uptake and accumulation mechanisms of hexachloroplatinate(IV) ions in the unicellular alga, Pseudococcomyxa simplex.

Platinum uptake was examined by adding hexachloroplatinate(IV) solution to the unicellular alga Pseudococcomyxa simplex. After the addition of platinum solution ([Pt] = 100 mg/kg, pH 3.2-3.2) for a certain time, the cells were quickly frozen and subjected to µ-XRF (X-ray fluorescence) analysis using synchrotron X-rays. The beam size of approximately 1 micrometer allowed visualization of the platinum distribution within a single cell. On the other hand, we examined platinum uptake in enzyme-treated protoplasts and lyophilized cells and found that the platinum uptake concentrations in these samples were higher than in living in-vivo cells. Cell wall and cell metabolism were presumed to interfere with the uptake of hexachloroplatinate(IV) ions. All platinum ions taken up by the cells were reduced to divalent form. The effect of light on platinum addition was also investigated. When platinum was added under light conditions, some samples showed higher platinum accumulation than under shade conditions.

Evaluating Mass Spectrometry-Based Hydroxyl Radical Protein Footprinting of a Benchtop Flash Oxidation System against a Synchrotron X-ray Beamline.

Hydroxyl radical protein footprinting (HRPF) using synchrotron X-ray radiation (XFP) and mass spectrometry is a well-validated structural biology method that provides critical insights into macromolecular structural dynamics, such as determining binding sites, measuring affinity, and mapping epitopes. Numerous alternative sources for generating the hydroxyl radicals (•OH) needed for HRPF, such as laser photolysis and plasma irradiation, complement synchrotron-based HRPF, and a recently developed commercially available instrument based on flash lamp photolysis, the FOX system, enables access to laboratory benchtop HRPF. Here, we evaluate performing HRPF experiments in-house with a benchtop FOX instrument compared to synchrotron-based X-ray footprinting at the NSLS-II XFP beamline. Using lactate oxidase (LOx) as a model system, we carried out •OH labeling experiments using both instruments, followed by nanoLC-MS/MS bottom-up peptide mass mapping. Experiments were performed under high glucose concentrations to mimic the highly scavenging conditions present in biological buffers and human clinical samples, where less •OH are available for reaction with the biomolecule(s) of interest. The performance of the FOX and XFP HRPF methods was compared, and we found that tuning the •OH dosage enabled optimal labeling coverage for both setups under physiologically relevant highly scavenging conditions. Our study demonstrates the complementarity of FOX and XFP labeling approaches, demonstrating that benchtop instruments such as the FOX photolysis system can increase both the throughput and the accessibility of the HRPF technique.

XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures.

The combination of X-ray free-electron lasers (XFELs) with serial femtosecond crystallography represents cutting-edge technology in structural biology, allowing the study of enzyme reactions and dynamics in real time through the generation of `molecular movies'. This technology combines short and precise high-energy X-ray exposure to a stream of protein microcrystals. Here, the XFEL structure of carbonic anhydrase II, a ubiquitous enzyme responsible for the interconversion of CO2 and bicarbonate, is reported, and is compared with previously reported NMR and synchrotron X-ray and neutron single-crystal structures.

A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst.

With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.

The human middle ear in motion: 3D visualization and quantification using dynamic synchrotron-based X-ray imaging.

The characterization of the vibrations of the middle ear ossicles during sound transmission is a focal point in clinical research. However, the small size of the structures, their micrometer-scale movement, and the deep-seated position of the middle ear within the temporal bone make these types of measurements extremely challenging. In this work, dynamic synchrotron-based X-ray phase-contrast microtomography is used on acoustically stimulated intact human ears, allowing for the three-dimensional visualization of entire human eardrums and ossicular chains in motion. A post-gating algorithm is used to temporally resolve the fast micromotions at 128 Hz, coupled with a high-throughput pipeline to process the large tomographic datasets. Seven ex-vivo fresh-frozen human temporal bones in healthy conditions are studied, and the rigid body motions of the ossicles are quantitatively delineated. Clinically relevant regions of the ossicular chain are tracked in 3D, and the amplitudes of their displacement are computed for two acoustic stimuli.

Deep residual networks for crystallography trained on synthetic data.

The use of artificial intelligence to process diffraction images is challenged by the need to assemble large and precisely designed training data sets. To address this, a codebase called Resonet was developed for synthesizing diffraction data and training residual neural networks on these data. Here, two per-pattern capabilities of Resonet are demonstrated: (i) interpretation of crystal resolution and (ii) identification of overlapping lattices. Resonet was tested across a compilation of diffraction images from synchrotron experiments and X-ray free-electron laser experiments. Crucially, these models readily execute on graphics processing units and can thus significantly outperform conventional algorithms. While Resonet is currently utilized to provide real-time feedback for macromolecular crystallography users at the Stanford Synchrotron Radiation Lightsource, its simple Python-based interface makes it easy to embed in other processing frameworks. This work highlights the utility of physics-based simulation for training deep neural networks and lays the groundwork for the development of additional models to enhance diffraction collection and analysis.

X-ray phase contrast reveals soft tissue and shell growth lines in mollusks.

High-resolution 3D imaging of species with exoskeletons such as shell-bearing mollusks typically involves destructive steps. Nondestructive alternatives are desirable since samples can be rare and valuable, and destructive steps are time-consuming and may distort the tissue. Here, we show for the first time that propagation-based phase-contrast X-ray imaging can significantly increase contrast in mollusks with intact shells. By using the recently upgraded monochromator at the SPring-8 BL20B2 synchrotron beamline, we imaged six species of mollusks, showing that X-ray phase contrast enhances soft-tissue contrast. Features that are almost invisible in conventional attenuation-based micro-computed tomography (micro-CT) are clearly reproduced with phase-contrast imaging under the same scan conditions. Furthermore, this method can reveal features such as growth rings in the shell and differentiate between calcite and aragonite crystal forms. Phase-contrast imaging can thus serve as a compelling alternative when destructive methods are not an option.

From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons.

Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump-probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.

Mini-GRID radiotherapy on the CLEAR very-high-energy electron beamline: collimator optimization, film dosimetry, and Monte Carlo simulations.

Objective.Spatially-fractionated radiotherapy (SFRT) delivered with a very-high-energy electron (VHEE) beam and a mini-GRID collimator was investigated to achieve synergistic normal tissue-sparing through spatial fractionation and the FLASH effect.Approach.A tungsten mini-GRID collimator for delivering VHEE SFRT was optimized using Monte Carlo (MC) simulations. Peak-to-valley dose ratios (PVDRs), depths of convergence (DoCs, PVDR ≤ 1.1), and peak and valley doses in a water phantom from a simulated 150 MeV VHEE source were evaluated. Collimator thickness, hole width, and septal width were varied to determine an optimal value for each parameter that maximized PVDR and DoC. The optimized collimator (20 mm thick rectangular prism with a 15 mm × 15 mm face with a 7 × 7 array of 0.5 mm holes separated by 1.1 mm septa) was 3D-printed and used for VHEE irradiations with the CERN linear electron accelerator for research beam. Open beam and mini-GRID irradiations were performed at 140, 175, and 200 MeV and dose was recorded with radiochromic films in a water tank. PVDR, central-axis (CAX) and valley dose rates and DoCs were evaluated.Main results.Films demonstrated peak and valley dose rates on the order of 100 s of MGy/s, which could promote FLASH-sparing effects. Across the three energies, PVDRs of 2-4 at 13 mm depth and DoCs between 39 and 47 mm were achieved. Open beam and mini-GRID MC simulations were run to replicate the film results at 200 MeV. For the mini-GRID irradiations, the film CAX dose was on average 15% higher, the film valley dose was 28% higher, and the film PVDR was 15% lower than calculated by MC.Significance.Ultimately, the PVDRs and DoCs were determined to be too low for a significant potential for SFRT tissue-sparing effects to be present, particularly at depth. Further beam delivery optimization and investigations of new means of spatial fractionation are warranted.

Few-seconds range verification with short-lived positron emitters in carbon ion therapy.

In-beam PET (Positron Emission Tomography) is one of the most precise techniques for in-vivo range monitoring in hadron therapy. Our objective was to demonstrate the feasibility of a short irradiation run for range verification before a carbon-ion treatment. To do so a PMMA target was irradiated with a 220 MeV/u carbon-ion beam and annihilation coincidences from short-lived positron emitters were acquired after irradiations lasting 0.6 s. The experiments were performed at the synchrotron-based facility CNAO (Italian National Center of Oncological Hadrontherapy) by using the INSIDE in-beam PET detector. The results show that, with 3·107 carbon ions, the reconstructed positron emitting nuclei distribution is in good agreement with the predictions of a detailed FLUKA Monte Carlo study. Moreover, the radio-nuclei production is sufficiently abundant to determine the average ion beam range with a σ of 1 mm with a 6 s measurement of the activity distribution. Since the data were acquired when the beam was off, the proposed rapid calibration method can be applied to hadron beams extracted from accelerators with very different time structures.

In Operando Analysis of Milk-Based Oral Formulations during Digestion Using Synchrotron Small-Angle X-ray Scattering Coupled to Low-Frequency Raman Spectroscopy.

A low-frequency Raman (LFR) probe was coupled to an in-line small-angle X-ray scattering (SAXS) beamline to test the capabilities of a combinatory approach for the determination of lipid and drug behavior during the enzymatic lipolysis of milk-based oral formulations. Cinnarizine was used as the model drug, and its solubilization dynamics as well as its potential impact on the supramolecular structures formed by the digestion products of bovine milk were evaluated from the perspective of both techniques. The SAXS data were superior in distinguishing various liquid crystalline assemblies formed during the digestion process, with LFR providing complementary information regarding the formation of calcium soaps. On the other hand, studying changes in the LFR domain allowed the differentiation of drug solubilization and precipitation; processes that were less clear from the X-ray scattering data. Given the relative simplicity of the combined experimental setup, these results highlight the advantages that the combination of the two techniques can provide for understanding and developing new lipid-based formulations and will help to translate the results obtained at synchrotron facilities to routine analysis procedures in laboratory/industry-based environments.