Synchrotron infrared nanospectroscopy in fourth-generation storage rings.

Fourth-generation synchrotron storage rings represent a significant milestone in synchrotron technology, offering outstandingly bright and tightly focused X-ray beams for a wide range of scientific applications. However, due to their inherently tight magnetic lattices, these storage rings have posed critical challenges for accessing lower-energy radiation, such as infrared (IR) and THz. Here the first-ever IR beamline to be installed and to operate at a fourth-generation synchrotron storage ring is introduced. This work encompasses several notable advancements, including a thorough examination of the new IR source at Sirius, a detailed description of the radiation extraction scheme, and the successful validation of our optical concept through both measurements and simulations. This optimal optical setup has enabled us to achieve an exceptionally wide frequency range for our nanospectroscopy experiments. Through the utilization of synchrotron IR nanospectroscopy on biological and hard matter samples, the practicality and effectiveness of this beamline has been successfully demonstrated. The advantages of fourth-generation synchrotron IR sources, which can now operate with unparalleled stability as a result of the stringent requirements for producing low-emittance X-rays, are emphasized.

Molecular and cellular basis of hyperassembly and protein aggregation driven by a rare pathogenic mutation in DDX3X.

Current studies estimate that 1-3% of females with unexplained intellectual disability (ID) present de novo splice site, nonsense, frameshift, or missense mutations in the DDX3X protein (DEAD-Box Helicase 3 X-Linked). However, the cellular and molecular mechanisms by which DDX3X mutations impair brain development are not fully comprehended. Here, we show that the ID-linked missense mutation L556S renders DDX3X prone to aggregation. By using a combination of biophysical assays and imaging approaches, we demonstrate that this mutant assembles solid-like condensates and amyloid-like fibrils. Although we observed greatly reduced expression of the mutant allele in a patient who exhibits skewed X inactivation, this appears to be enough to sequestrate healthy proteins into solid-like ectopic granules, compromising cell function. Therefore, our data suggest ID-linked DDX3X L556S mutation as a disorder arising from protein misfolding and aggregation.

Correlations between lignin content and structural robustness in plants revealed by X-ray ptychography.

Lignin is a heterogeneous aromatic polymer responsible for cell wall stiffness and protection from pathogen attack. However, lignin represents a bottleneck to biomass degradation due to its recalcitrance related to the natural cell wall resistance to release sugars for fermentation or further processing. A biological approach involving genetics and molecular biology was used to disrupt lignin pathway synthesis and decrease lignin deposition. Here, we imaged three-dimensional fragments of the petioles of wild type and C4H lignin mutant Arabidopsis thaliana plants by synchrotron cryo-ptychography. The three-dimensional images revealed the heterogeneity of vessels, parenchyma, and fibre cell wall morphologies, highlighting the relation between disturbed lignin deposition and vessel implosion (cell collapsing and obstruction of water flow). We introduce a new parameter to accurately define cell implosion conditions in plants, and we demonstrate how cryo-ptychographic X-ray computed tomography (cryo-PXCT) provides new insights for plant imaging in three dimensions to understand physiological processes.

Phase Diagrams and Structural Characterization of Mixtures of Silicone Surfactants + Silicone Oils + Water.

Silicone surfactants display unique properties and are widely employed in pharmaceutical and cosmetic products. In this work, we study water incorporation into silicone oils using silicone surfactants. Despite their importance, there are only a few studies reporting their phase equilibrium and structural characterization. Here, we determined the phase diagram of systems containing silicone oils, silicone surfactants, and water. In particular, we investigated the self-assembly behavior of two siloxane surfactants with the different hydrophilic-lipophilic balance: M(D'E7OH)M and MD18(D'3E18OAc)M and two silicone oils (cyclic oil-D4 and linear oil-MD15M). The phase behavior of the mixtures was investigated through optical inspection and structural characterization of aggregated states (microemulsions and mesophases) using small angle X-ray scattering (SAXS). These water-in-oil microemulsions or bicontinuous microemulsions incorporated a maximum amount of approximately 20 wt % water for the two surfactants with cyclic oil. A similar behavior was also identified with linear silicone oil, though with smaller water contents. We also observed the formation of anisotropic states, with a predominance of lamellar phases and a small region of a hexagonal phase. A quantitative analysis of the SAXS curves in the lamellar region reveals that this mesophase swells continuously after the addition of water lamellar periods ranging from 50 Å (with 18 wt % water) to 64 Å (with 40 wt % water). Our results confirm and expand the earlier literature on similar compounds, indicating their potential in incorporating water into silicone mixtures and forming interesting mesophases. Accompanying this characterization, we also report a comprehensive and systematic set of structural details for the different systems (microemulsions, bicontinuous phases and mesophases) formed by these mixtures, derived from the SAXS measurements.

High-resolution synchrotron-based X-ray microtomography as a tool to unveil the three-dimensional neuronal architecture of the brain.

The assessment of neuronal number, spatial organization and connectivity is fundamental for a complete understanding of brain function. However, the evaluation of the three-dimensional (3D) brain cytoarchitecture at cellular resolution persists as a great challenge in the field of neuroscience. In this context, X-ray microtomography has shown to be a valuable non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens, arisen as a new method for deciphering the cytoarchitecture and connectivity of the brain. In this work we present a method for imaging whole neurons in the brain, combining synchrotron-based X-ray microtomography with the Golgi-Cox mercury-based impregnation protocol. In contrast to optical 3D techniques, the approach shown here does neither require tissue slicing or clearing, and allows the investigation of several cells within a 3D region of the brain.

Low-aberration beamline optics for synchrotron infrared nanospectroscopy.

Synchrotron infrared nanospectroscopy is a recently developed technique that enables new possibilities in the broadband chemical analysis of materials in the nanoscale, far beyond the diffraction limit in this frequency domain. Synchrotron infrared ports have exploited mainly the high brightness advantage provided by electron storage rings across the whole infrared range. However, optical aberrations in the beam produced by the source depth of bending magnet emission at large angles prevent infrared nanospectroscopy to reach its maximum capability. In this work we present a low-aberration optical layout specially designed and constructed for a dedicated synchrotron infrared nanospectroscopy beamline. We report excellent agreement between simulated beam profiles (from standard wave propagation and raytracing optics simulations) with experimental measurements. We report an important improvement in the infrared nanospectroscopy experiment related to the improved beamline optics. Finally, we demonstrate the performance of the nanospectroscopy endstation by measuring a hyperspectral image of a polar material and we evaluate the setup sensitivity by measuring ultra-thin polymer films down to 6 nm thick.

The coherent radiation fraction of low-emittance synchrotrons.

In this work the coherence properties of the synchrotron radiation beam from an X-ray undulator in a fourth-generation storage ring are analyzed. A slightly focused X-ray beam is simulated using a wavefront propagation through a non-redundant array of slits and the mutual coherence function is directly obtained and compared with the Gaussian-Schell approximation. The numerical wave propagation and the approximate analytical approaches are shown to agree qualitatively, and it is also shown that, when the coherent fraction is selected by a finite aperture before the focusing element, even achromatic focusing systems like total reflection mirrors become slightly chromatic. This effect is also well accounted for in the Gaussian-Schell model. The wavefront propagation simulation through the non-redundant array was repeated with an imperfect mirror demonstrating that, although the wavefront is distorted, its coherent length is practically unchanged.

Nanostructural reorganization of bacterial cellulose by ultrasonic treatment.

In this work, bacterial cellulose was subjected to a high-power ultrasonic treatment for different time intervals. The morphological analysis, scanning electron microscopy, and atomic force microscopy revealed that this treatment changed the width and height of the microfibrillar ribbons and roughness of their surface, originating films with new nanostructures. Differential thermal analysis showed a higher thermal stability for ultrasonicated samples with a pyrolysis onset temperature of 208 degrees C for native bacterial cellulose and 250 and 268 degrees C for the modified samples. The small-angle X-ray scattering experiments demonstrated that the treatment with ultrasound increased the thickness of the ribbons, while wide-angle X-ray scattering experiments demonstrated that the average crystallite dimension and the degree of crystallinity also increased. A model is proposed where the thicker ribbons and crystallites result from the fusion of neighboring ribbons due to cavitation effects.

Effect of the alkaline treatment on the ultrastructure of C-type starch granules.

The effect of alkaline treatment on the ultrastructure of C-type starch granules was investigated during the alkaline extraction of Araucaria angustifolia (pinhao) starch. The efficiency in protein removal was evaluated using intrinsic fluorescence and Kjeldahl's method. In parallel, morphological changes of starch granules were observed using scanning electron microscopy and atomic force microscopy. The starch crystallinity was monitored by wide-angle X-ray scattering and the lamellar structure was studied by small-angle X-ray scattering (SAXS). The paracrystalline model was employed to interpret the SAXS curves. It was found that the granular organization was significantly altered when alkaline solutions were used during the extraction. A partial degradation of B-type allomorph of starch and a significant compression of semicrystalline growth rings were observed.

Correlated disorder in random block copolymers.

We study the effect of a random Flory-Huggins parameter in a symmetric diblock copolymer melt which is expected to occur in a copolymer where one block is near its structural glass transition. In the clean limit the microphase segregation between the two blocks causes a weak, fluctuation induced first order transition to a lamellar state. Using a renormalization group approach combined with the replica trick to treat the quenched disorder, we show that beyond a critical disorder strength, which depends on the length of the polymer chain, the character of the transition is changed. The system becomes dominated by strong randomness and a glassy rather than an ordered lamellar state occurs. A renormalization of the effective disorder distribution leads to nonlocal disorder correlations that reflect strong compositional fluctuation on the scale of the radius of gyration of the polymer chains. The reason for this behavior is shown to be the chain length dependent role of critical fluctuations, which are less important for shorter chains and become increasingly more relevant as the polymer length increases and the clean first order transition becomes weaker.