SAXS Methods Research Articles

ZBP1 condensate formation synergizes Z-NAs recognition and signal transduction

Z-DNA binding protein 1 (ZBP1) is a crucial player in the intracellular recognition of Z-form nucleic acids (Z-NAs) through its Zαβ domain, initiating downstream interactions with RIPK1 and RIPK3 via RHIM domains. This engagement leads to the assembly of PANoptosomes, ultimately inducing programmed cell death to curb pathogen dissemination. How Zαβ and RHIM domain cooperate to trigger Z-NAs recognition and signal transduction remains unclear. Here, we show that ZBP1 condensate formation facilitates Z-NAs binding and antiviral signal transduction. The ZBP1 Zαβ dimerizes in a concentration-dependent manner, forming characteristic condensates in solutions evidenced by DLS and SAXS methods. ZBP1 exhibits a binding preference for 10-bp length CG (10CG) DNA and Z-RNA ligand, which in turn enhanced Zαβ dimerization, expediting the formation of droplet condensates in vitro and amyloid-like puncta in cells. Subsequent investigations reveal that Zαβ could form condensates with liquid-liquid phase separation property upon HSV and IAV infections, while full-length ZBP1 forms amyloid-like puncta with or without infections. Furthermore, ZBP1 RHIM domains show typical amyloidal fibril characterizations and cross-polymerize with RIPK1 depending on the core motif of 206IQIG209, while mutated ZBP1 could impede necroptosis and antiviral immunity in HT-29 cells. Thus, ZBP1 condensate formation facilitates the recognition of viral Z-NAs and activation of downstream signal transduction via synergic action of different domains, revealing its elaborated mechanism in innate immunity.

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.

The effect of chemical composition and heat parameter on Nano-sized precipitate dispersion characterization in ODS steels

Oxide dispersion strengthened (ODS) supersaturated solid solution alloy powders with different Y/Ti atomic ratios were formed by mechanical alloying (MA) method and then heat treated under different conditions. The morphology, phase composition, and particle size distribution were researched. The precipitate distribution densities and hardness values of alloy powders after heat treatment were measured at the same time by the SAXS method and hard tester. The results show that the morphology of MA alloy powders is irregular in shape and only a small amount of MA alloy powders is bigger than 30 μm. During the MA process, alloy elements are solid solutions in the matrix. The work-harden effect of alloy powders formed in the MA process would be eliminated during the heat treatment process. The chemical composition and heat treatment parameters are crucial effects on nano-sized precipitate distribution characterization in ODS steels. The ODS sample with a Y/Ti atomic ratio of 0.99 has the highest distribution density of oxide precipitates at 1.89×1022/m3 resulting in the highest hardness value during the heat treatment process. The sample with a Y/Ti atomic ratio of 0.42 has the highest distribution density of nanoclusters 7.32×1023/m3.

Synthesis and study of some physicochemical features of Co-Pt nanostructured system

In the work by methods of XRD, TEM, SAED, XPS combined with mass-spectrometry of gaseous products, SAXS, and elemental analysis of samples the phase compositions and morphology of particles of nanostructured Co-Pt system synthesized by the method of reduction of hydrazine-hydrate aqueous solutions of precursors were studied (in the region rich in Pt for the first time). It was found that in the composition range up to ≈ 60 at. % Co. XRD-analysis of synthesized samples fixes as the only FCC phase of solid solution of Co in Pt, with the established upper limit of solubility %18±1 at. At the content of Co above the limit, along with it, the X-ray diffraction unregistered phases with the content of Co above the limit in solid solution are also formed. Their presence was confirmed by the SAXS method, and their metallic nature (not oxide-hydroxide) nature follows from the results of XRD, SAED. When FCC phase formed metal reduction process proceeded directly without cobalt hydroxides forming. According to results of XPS with the Ar-etching of samples there were internal platinum-rich sub-regions in Co-Pt nanoalloys.

Sol-Gel-Derived Functional Coatings for Pre-Sowing Seed Treatment

The superatomic structure of film-forming sols obtained by the acid hydrolysis of tetraethoxysilane (TEOS) in an aqueous medium (free of organic solvents) was studied using the SAXS method. The formation of nanoparticles (NPs) was confirmed in alcohol-free silica sols with both a low (1 vol. %) content of TEOS and a high (10 vol. %) content of TEOS, hydrolyzed in an aqueous-alcoholic medium. A trimodal size distribution was revealed for the resulting NPs, with radii ranging from less than 1 nm to ~11 nm. The volume fraction of NPs tends to grow with increases in TEOS concentration, as well as with the introduction of magnetic NPs of iron oxides into silica sols. The synthesized silica sols and suspensions based on silica sols with FexOy NPs were used for the pre-sowing treatment of white and cauliflower cabbage seeds in order to provide a functional coating on their surfaces, thereby improving seed germination, stimulating their growth in the early stages of development, and suppressing the effect of phytopathogens. The effect of the pre-sowing seed treatment in sol-gel compositions on seed germination and the growth characteristics of plant seedlings is analyzed, including the influence of iron-oxide magnetic NPs’ compositions and concentrations in silica sols.

Release Kinetics of Potassium, Calcium, and Iron Cations from Carboxymethyl Cellulose Hydrogels at Different pH Values.

In an in-depth study of the mechanism of cation release from carboxymethyl cellulose hydrogels synthesized through Schiff base reaction, we analyze the differences in the release kinetics of potassium, calcium, and iron cations with Peleg model at pH values of pH 3.5 and pH 8.5 using ICP-OES (inductively coupled plasma optical emission spectroscopy) technique.

Oxyfluoroniobate glasses in the ZnNbOF5-BaF2-InF3 system

Glasses in the ZnNbOF5–BaF2–InF3 and ZnNbOF5-BaF2 systems were produced using the ZnNbOF5•6H2O compound. The structure, thermal and luminescent properties of the obtained glasses were studied with IR-, Raman, SAXS, luminescent spectroscopy methods, calorimetry and X-ray diffraction. The highest range of thermal stability and resistance of glass to crystallization has been established for the glass of 20ZnNbOF5–40BaF2–40InF3 composition. This value is an order of magnitude higher than in glasses of the same system, but not containing InF3. Glasses networks are formed from polyhedra of InF6, NbO2F4 and NbO3F3. For all glasses containing InF3, photoluminescence contribution which depends on the concentration of indium trifluoride in the glass was recorded. This contribution corresponds to the emission levels of 542, 573, 673, 751 nm. Luminescent properties are shown by glasses in which nanoobjects (nanoinhomogeneities) in size of 9-13 nm were detected by SAXS method.

Selected advances in small-angle scattering and applications they serve in manufacturing, energy and climate change.

Innovations in small-angle X-ray and neutron scattering (SAXS and SANS) at major X-ray and neutron facilities offer new characterization tools for researching materials phenomena relevant to advanced applications. For SAXS, the new generation of diffraction-limited storage rings, incorporating multi-bend achromat concepts, dramatically decrease electron beam emittance and significantly increase X-ray brilliance over previous third-generation sources. This results in intense X-ray incident beams that are more compact in the horizontal plane, allowing significantly improved spatial resolution, better time resolution, and a new era for coherent-beam SAXS methods such as X-ray photon correlation spectroscopy. Elsewhere, X-ray free-electron laser sources provide extremely bright, fully coherent, X-ray pulses of <100 fs and can support SAXS studies of material processes where entire SAXS data sets are collected in a single pulse train. Meanwhile, SANS at both steady-state reactor and pulsed spallation neutron sources has significantly evolved. Developments in neutron optics and multiple detector carriages now enable data collection in a few minutes for materials characterization over nanometre-to-micrometre scale ranges, opening up real-time studies of multi-scale materials phenomena. SANS at pulsed neutron sources is becoming more integrated with neutron diffraction methods for simultaneous structure characterization of complex materials. In this paper, selected developments are highlighted and some recent state-of-the-art studies discussed, relevant to hard matter applications in advanced manufacturing, energy and climate change.

Properties of Nanocomposites Based on Platinum Nanoparticles Stabilized by Chitosan

AbstractPlatinum nanoparticles were obtained chemically in acetic acid solutions of chitosan from the precursor H2PtCl6 using sodium borohydride as a reducing agent with simultaneous UV irradiation. The compositions were studied by SAXS, TEM, dynamic light scattering, FTIR‐spectroscopy, differential scanning calorimetry, dynamic mechanical analysis, and atomic force microscopy. Nanoparticles are characterized by a narrowly dispersed size distribution while the effect of the conformation of chitosan macromolecules on their characteristics is manifested. The SAXS method showed that in a chitosan solution with a semi‐flexible coil conformation of macromolecules, 96.8 % of the formed nanoparticles are characterized by an average radius of 1.4 nm. According to the TEM results, platinum nanoparticles are characterized by a crystal structure and a particle diameter of about 1.3–5.0 nm. A different picture is observed for platinum nanoparticles formed in chitosan with the rigid rod conformation of macromolecules – only 91 % of platinum nanoparticles had an average radius of 1.4 nm. The TEM method showed these nanoparticles turned out to be about 1 nm in size, and they did not crystallize, but remained amorphous. The introduction of platinum nanoparticles into the polysaccharide matrix significantly shifts the glass transition temperature of chitosan toward lower values by 20 and 10 °C respectively, and increases the tensile strength of the composites by 35 MPa.

Influence of Stress Field and Temperature Field on Residual Stress of 2A14 Aluminum Alloy Based on In Situ SAXS Method.

In this paper, based on in situ synchrotron radiation SAXS technology, the effects of stress field, temperature field and thermo-mechanical coupling conditions on the evolution of residual stress are discussed, respectively. The results show that the continuous increase of the external load led to the increase of the residual stress perpendicular to the tensile direction of the 2A14 aluminum alloy, and when the external load closed to the yield strength, the change of the residual stress was no longer significant. Under the action of temperature, the residual stress of 2A14 aluminum alloy reduced after the process of heating-holding-cooling. Under the action of thermo-mechanical coupling, the recovery effect of aluminum alloy was triggered, the energy storage of deformation was released, the lattice strain was reduced and the residual stress introduced by external load was reduced.

Structural Characteristics of the 5'-Terminal Region of Mouse p53 mRNA and Identification of Proteins That Bind to This mRNA Region.

A mouse model has often been used in studies of p53 gene expression. Detailed interpretation of functional studies is, however, hampered by insufficient knowledge of the impact of mouse p53 mRNA’s structure and its interactions with proteins in the translation process. In particular, the 5′-terminal region of mouse p53 mRNA is an important region which takes part in the regulation of the synthesis of p53 protein and its N-truncated isoform Δ41p53. In this work, the spatial folding of the 5′-terminal region of mouse p53 mRNA and its selected sub-fragments was proposed based on the results of the SAXS method and the RNAComposer program. Subsequently, RNA-assisted affinity chromatography was used to identify proteins present in mouse fibroblast cell lysates that are able to bind the RNA oligomer, which corresponds to the 5′-terminal region of mouse p53 mRNA. Possible sites to which the selected, identified proteins can bind were proposed. Interestingly, most of these binding sites coincide with the sites determined as accessible to hybridization of complementary oligonucleotides. Finally, the high binding affinity of hnRNP K and PCBP2 to the 5′-terminal region of mouse p53 mRNA was confirmed and their possible binding sites were proposed.

Microstructure development of PEBA and its impact on autoclave foaming behavior and inter-bead bonding of EPEBA beads

Expanded poly(ether-block-amide) (EPEBA) bead foams are a new class of advanced thermoplastic elastomer foams with low density and high resilience. Steam-chest molding realizes the fabrication of the molded EPEBA bead foams with complex geometry. However, the evolution of polymer microstructure in autoclave foaming process and the bonding mechanism behind the steam-chest molding of EPEBA beads are still unclear. In this work, the microstructure development of PEBA was characterized by DSC, SAXS and rheological methods. Then, EPEBA beads with an expansion ratio higher than 25-fold were prepared by autoclave foaming, and the molded EPEBA bead foams with a density lower than 0.15 g/cm3 and a resilience higher than 70% were produced by steam-chest molding. According to the change about thermal properties of EPEBA beads before and after steam-chest molding, a possible inter-bead bonding mechanism during EPEBA beads molding was proposed. The amorphous soft segments and melted low-ordered hard segments promoted the welding process. However, the well-ordered hard segments hindered the interdiffusion of polymer chains at the interface, which leaded to the reduced tensile strength and the narrowed molding temperature window of EPEBA bead foams.

Photosensitive titanium-containing interpenetrating polymer networks for photonics

Kinetic investigations of titanium-containing interpenetrating polymer networks (Ti-IPNs) formation based on cross-linked polyurethane and Ti-containing copolymer (Ti-CP) were carried out using differential calorimetry method. Analysis by the SAXS method revealed that the systems possessed nanosized regions of heterogeneity. The increase of (–TiO2–) fragments content led to increase of both overall level of heterogeneity and of Tg of Ti-СP component. Ti-IPNs are optically transparent with optical transparency coefficient value up to 90–91% at 650 nm. The reverse visible darkening at UV-irradiation was observed for Ti-IPNs, thereby allowing their application in optical data recording on exposure to laser radiation.

Cover Feature: Fractal Features of the Catalytic Performances of Bimodal Mesoporous Silica‐Supported Organocatalysts Derived from Bipyridine‐Proline for Asymmetric Aldol Reaction (Asian J. Org. Chem. 2/2022)

Heterogeneous catalysis is a promising way to developing benign processes in asymmetric aldol reaction, in which the catalytic performance can be precisely modulated by bipyridine-proline loaded catalyst. Herein, the bimodal mesoporous silicas could provide controlled pore channels and suitable modified surfaces for reactants and organic catalysts. Therefore, their reactivity and selectivity, as well as recyclability potential could be improved. Besides, the fractal features of the heterogeneous catalysts were elucidated in-depth by SAXS method. More information can be found in the Full Paper by Jihong Sun et al.

Comparison of mesoporous fractal characteristics of silica-supported organocatalysts derived from bipyridine-proline and resultant effects on the catalytic asymmetric aldol performances.

Three kinds of the bipyridine-proline chiral ligands as highly active species were successfully introduced on Zn-modified mesoporous silica nanomaterials (BMMs, MCM-41, and SBA-15) via the covalent attachment and coordination methods. Their microstructural features and physicochemical properties were extensively characterized via XRD patterns, SEM/TEM images, TGA profiles, FT-IR and UV-Vis spectra. In particular, their fractal features, the pair distance distribution function, and the Porod plots were evaluated thoroughly on the basis of the SAXS data. Meanwhile, their catalytic performances for asymmetric aldol reactions between p-nitrobenzaldehyde and cyclohexanone were evaluated. The results indicated that the bimodal mesoporous BMMs-based samples with short worm-like mesoporous channels possessed both mass and surface fractal features, whereas the MCM-41- and SBA-15-based samples with long-range ordered structures only showed surface fractal features. The influences of various reaction parameters, including the textures of the mesoporous silicas, the structures of the used chiral ligands, and the molecular volumes of aldehydes, on the catalytic activities (yield) and stereoselectivities (dr and ee) were investigated thoroughly. The results showed satisfactory activities (yields) and better stereoselectivity (dr and ee) in comparison with the homogeneous catalytic system using Z as the catalysts. In particular, the 3rd recycle catalytic performances of the Z-immobilized heterogeneous catalysts retained high catalytic yields (around 80%) and ee values of 28%. These phenomena were well interpreted by the essential relationships between the fractal characteristics of these heterogeneous catalysts and their catalytic activities.

Poly(C)-binding Protein 2 Regulates the p53 Expression via Interactions with the 5'-Terminal Region of p53 mRNA.

The p53 protein is one of the major transcriptional factors which guards cell homeostasis. Here, we showed that poly(C)-binding protein 2 (PCBP2) can bind directly to the 5′ terminus of p53 mRNA by means of electrophoretic mobility shift assay. Binding sites of PCBP2 within this region of p53 mRNA were mapped using Pb2+-induced cleavage and SAXS methods. Strikingly, the downregulation of PCBP2 in HCT116 cells resulted in a lower level of p53 protein under normal and stress conditions. Quantitative analysis of p53 mRNA in PCBP2-downregulated cells revealed a lower level of p53 mRNA under normal conditions suggesting the involvement of PCBP2 in p53 mRNA stabilisation. However, no significant change in p53 mRNA level was observed upon PCBP2 depletion under genotoxic stress. Moreover, a higher level of p53 protein in the presence of rapamycin or doxorubicin and the combination of both antibiotics was noticed in PCBP2-overexpressed cells compared to control cells. These observations indicate the potential involvement of PCBP2 in cap-independent translation of p53 mRNA especially occurring under stress conditions. It has been postulated that the PCBP2 protein is engaged in the enhancement of p53 mRNA stability, probably via interacting with its 3′ end. Our data show that under stress conditions PCBP2 also modulates p53 translation through binding to the 5′ terminus of p53 mRNA. Thus PCBP2 emerges as a double-function factor in the p53 expression.

Characterization and Antitumoral Activity of Biohybrids Based on Turmeric and Silver/Silver Chloride Nanoparticles.

The phyto-development of nanomaterials is one of the main challenges for scientists today, as it offers unusual properties and multifunctionality. The originality of our paper lies in the study of new materials based on biomimicking lipid bilayers loaded with chlorophyll, chitosan, and turmeric-generated nano-silver/silver chloride particles. These materials showed a good free radical scavenging capacity between 76.25 and 93.26% (in vitro tested through chemiluminescence method) and a good antimicrobial activity against Enterococcus faecalis bacterium (IZ > 10 mm). The anticancer activity of our developed bio-based materials was investigated against two cancer cell lines (human colorectal adenocarcinoma cells HT-29, and human liver carcinoma cells HepG2) and compared to one healthy cell line (human fibroblast BJ cell line). Cell viability was evaluated for all prepared materials after a 24 h treatment and was used to select the biohybrid with the highest therapeutic index (TI); additionally, the hemolytic activity of the samples was also evaluated. Finally, we investigated the morphological changes induced by the developed materials against the cell lines studied. Biophysical studies on these materials were done by correlating UV–Vis and FTIR absorption spectroscopy, with XRD, SANS, and SAXS methods, and with information provided by microscopic techniques (AFM, SEM/EDS). In conclusion, these “green” developed hybrid systems are an important alternative in cancer treatment, and against health problems associated with drug-resistant infections.

Relation of Fractal Characteristics with Structural Parameters of Nanosized ZrO2 Determined by Various Methods

The fractal dimensions of nanodispersed zirconia determined by the BET and SAXS methods are compared. The fractal dimensions were shown to depend on the characteristic dimensions of the surface areas determined by different methods. A method for calculating the surface fractal dimension using the difference between the specific surface obtained by the BET and SAXS methods is proposed.

Silica nanoparticle agglomeration studies under physiological conditions using dynamic SAXS methods

Silica nanoparticle agglomeration studies under physiological conditions using dynamic SAXS methods

Synthesis, structure and crystallization of glasses in the CdNbOF5–BaF2–InF3 system

The glasses in the CdNbOF 5 –BaF 2 –InF 3 system were obtained. The glass structure, thermal behaviour and crystallization were investigated by the IR spectroscopy, DSC, XRD and SAXS methods. The NbO 2 F 4 3− and InF 6 3− ions form mixed networks of glasses. For all of the glasses, the cubic phase of CdF 2 was found in the crystallization products. Upon heating, the crystalline phase of CdF 2 first appeared in the glasses. It was demonstrated that transparent glass-ceramic samples could be obtained by thermal treatment of the glasses in the CdNbOF 5 –BaF 2 –InF 3 system.