Medium-energy microprobe station at the SXRMB of the CLS

XANES reference library of sulphur-containing compounds for biological research: a status report from the ASTRA beamline at the SOLARIS National Synchrotron Radiation Centre

Sulphur is present in a vast multitude of biological compounds, and X-ray absorption spectroscopy (XAS) is a powerful and well-established characterization technique to study the local atomic environment of this chemical element in such systems in detail, with a high potential for advancing knowledge in medicine, biotechnology and environmental research. For this project, X-ray absorption near edge structure (XANES) spectroscopy at the sulphur K-absorption edge was used to investigate sulphur-containing compounds of biological interest at the ASTRA beamline (SOLARIS National Synchrotron Radiation Centre, Kraków, Poland). XANES provides valuable insights into the bonding environment of sulphur and thereby contributes to a deeper understanding of the structural characteristics and functional roles of sulphur in biological systems. The ASTRA beamline, specifically optimized for XAS in the tender energy range, offers ideal conditions for further research in this field, enabling detailed analysis of the composition and changes in sulphur containing compounds.

Applications of synchrotron light in seed research: an array of x-ray and infrared imaging methodologies

Synchrotron radiation (SR) provides a wide spectrum of bright light that can be tailored to test myriad research questions. SR provides avenues to illuminate structure and composition across scales, making it ideally suited to the study of plants and seeds. Here, we present an array of methodologies and the data outputs available at a light source facility. Datasets feature seed and grain from a range of crop species including Citrullus sp. (watermelon), Brassica sp. (canola), Pisum sativum (pea), and Triticum durum (wheat), to demonstrate the power of SR for advancing plant science. The application of SR micro-computed tomography (SR-µCT) imaging revealed internal seed microstructures and their three-dimensional morphologies in exquisite detail, without the need for destructive sectioning. Spectroscopy in the infrared spectrum probed sample biochemistry, detailing the spatial distribution of seed macronutrients such as lipid, protein and carbohydrate in the embryo, endosperm and seed coat. Methods using synchrotron X-rays, including X-ray absorption spectroscopy (XAS) and X-ray fluorescence (XRF) imaging revealed elemental distributions, to spatially map micronutrients in seed subcompartments and to determine their speciation. Synchrotron spectromicroscopy (SM) allowed chemical composition to be resolved at the nano-scale level. Diverse crop seed datasets showcase the range of structural and chemical insights provided by five beamlines at the Canadian Light Source, and the potential for synchrotron imaging for informing plant and agricultural research.

Development and application of a tender X-ray ptychographic coherent diffraction imaging system on BL27SU at SPring-8

Ptychographic coherent diffraction imaging (CDI) allows the visualization of both the structure and chemical state of materials on the nanoscale, and has been developed for use in the soft and hard X-ray regions. In this study, a ptychographic CDI system with pinhole or Fresnel zone-plate optics for use in the tender X-ray region (2-5 keV) was developed on beamline BL27SU at SPring-8, in which high-precision pinholes optimized for the tender energy range were used to obtain diffraction intensity patterns with a low background, and a temperature stabilization system was developed to reduce the drift of the sample position. A ptychography measurement of a 200 nm thick tantalum test chart was performed at an incident X-ray energy of 2.500 keV, and the phase image of the test chart was successfully reconstructed with approximately 50 nm resolution. As an application to practical materials, a sulfur polymer material was measured in the range of 2.465 to 2.500 keV including the sulfur K absorption edge, and the phase and absorption images were successfully reconstructed and the nanoscale absorption/phase spectra were derived from images at multiple energies. In 3 GeV synchrotron radiation facilities with a low-emittance storage ring, the use of the present system will allow the visualization on the nanoscale of the chemical states of various light elements that play important roles in materials science, biology and environmental science.

Synchrotron X-ray fluorescence microscopy-enabled elemental mapping illuminates the 'battle for nutrients' between plant and pathogen

Metal homeostasis is integral to normal plant growth and development. During plant-pathogen interactions, the host and pathogen compete for the same nutrients, potentially impacting nutritional homeostasis. Our knowledge of outcome of the interaction in terms of metal homeostasis is still limited. Here, we employed the X-ray fluorescence microscopy (XFM) beamline at the Australian Synchrotron to visualize and analyse the fate of nutrients in wheat leaves infected with Pyrenophora tritici-repentis, a necrotrophic fungal pathogen. We sought to (i) evaluate the utility of XFM for sub-micron mapping of essential mineral nutrients and (ii) examine the spatiotemporal impact of a pathogen on nutrient distribution in leaves. XFM maps of K, Ca, Fe, Cu, Mn, and Zn revealed substantial hyperaccumulation within, and depletion around, the infected region relative to uninfected control samples. Fungal mycelia were visualized as thread-like structures in the Cu and Zn maps. The hyperaccumulation of Mn in the lesion and localized depletion in asymptomatic tissue surrounding the lesion was unexpected. Similarly, Ca accumulated at the periphery of the symptomatic region and as microaccumulations aligning with fungal mycelia. Collectively, our results highlight that XFM imaging provides the capability for high-resolution mapping of elements to probe nutrient distribution in hydrated diseased leaves in situ.

Speciation of Phosphorus from Suspended Sediment Studied by Bulk and Micro-XANES

Mobilization, transformation, and bioavailability of fluvial suspended sediment-associated particulate phosphorus (PP) plays a key role in governing the surface water quality of agricultural catchment streams. Knowledge on the molecular P speciation of suspended sediment is valuable in understanding in-stream PP cycling processes. Such information enables the design of appropriate catchment management strategies in order to protect surface water quality and mitigate eutrophication. In this study, we investigated P speciation associated with fluvial suspended sediments from two geologically contrasting agricultural catchments. Sequential chemical P extractions revealed the operationally defined P fractions for the fluvial suspended sediments, with Tintern Abbey (TA) dominated by redox-sensitive P (PCBD), Al, and Fe oxyhydroxides P (PNaOH) and organic P (POrg) while Ballyboughal (BB) primarily composed of acid soluble P (PDetr), redox-sensitive P (PCBD), and loosely sorbed P (PNH4Cl). The dominant calcareous (Ca) elemental characteristic of BB suspended sediment with some concurrent iron (Fe) influences was confirmed by XRF which is consistent with the catchment soil types. Ca-P sedimentary compounds were not detected using bulk P K-edge XANES, and only P K-edge µ-XANES could confirm their presence in BB sediment. Bulk P K-edge XANES is only capable of probing the average speciation and unable to resolve Ca-P as BB spectra is dominated by organic P, which may suggest the underestimation of this P fraction by sequential chemical P extractions. Notably, µ-XANES of Ca K-edge showed consistent results with P K-edge and soil geochemical characteristics of both catchments where Ca-P bonds were detected, together with calcite in BB, while in TA, Ca-P bonds were detected but mostly as organic complexed Ca. For the TA site, Fe-P is detected using bulk P K-edge, which corresponds with its soil geochemical characteristics and sequential chemical P extraction data. Overall, P concentrations were generally lower in TA, which led to difficulties in Fe-P compound detection using µ-XANES of TA. Overall, our study showed that coupling sequential chemical P extractions with progressively more advanced spectroscopic techniques provided more detailed information on P speciation, which can play a role in mobilization, transformation, and bioavailability of fluvial sediment-associated P.

A portable data-collection system for soft x-ray absorption spectroscopy in the Shanghai Synchrotron Radiation Facility

Based on the Experimental Physics and Industrial Control System, a portable data-collection system for soft x-ray absorption spectroscopy has been developed at the BL02B and BL08U beamlines of the Shanghai Synchrotron Radiation Facility. The data-collection system can be used to carry out total electron yield (TEY) and total fluorescence yield (TFY) experiments simultaneously. The hardware consists of current preamplifiers, voltage-to-frequency converters, and a multi-channel counter, which are aimed at improving the signal-to-noise ratio. The control logic is developed using Python and Java. The novelty of this control system is its designed portability while being extensible and readable and having low noise and high real-time capabilities. The oxygen K-edge absorption spectra of SrTiO₃ were obtained using the TEY and TFY technology at the BL02B beamline. Furthermore, the TEY and TFY spectra of the relaxor ferroelectric single-crystal of lead magnesium niobate-lead titanate measured by the present data-collection system have lower peak-to-peak noise amplitude than the ones measured by using a picoammeter. The experimental results show that the spectral signal-to-noise ratio recorded by the present system is 5.7-12.4 dB higher than that with the picoammeter detector.

A micro-focusing and high-flux-throughput beamline design using a bending magnet for microscopic XAFS at the High Energy Photon Source

An optical design study of a bending-magnet beamline, based on multi-bend achromat storage ring lattices, at the High Energy Photon Source, to be built in Beijing, China, is described. The main purpose of the beamline design is to produce a micro-scale beam from a bending-magnet source with little flux loss through apertures. To maximize the flux of the focal spot, the synchrotron source will be 1:1 imaged to a virtual source by a toroidal mirror; a mirror pair will be used to collimate the virtual source into quasi-parallel light which will be refocused by a Kirkpatrick-Baez mirror pair. In the case presented here, a beamline for tender X-rays ranging from 2.1 keV to 7.8 keV, with a spot size of approximately 7 µm (H) × 6 µm (V) and flux up to 2 × 10¹² photons s^-1, can be achieved for the purpose of X-ray absorption fine-structure (XAFS)-related experiments, such as scanning micro-XAFS and full-field nano-XAFS.

Direct label-free imaging of brain tissue using synchrotron light: a review of new spectroscopic tools for the modern neuroscientist

The incidence of brain disease and brain disorders is increasing on a global scale. Unfortunately, development of new therapeutic strategies has not increased at the same rate, and brain diseases and brain disorders now inflict substantial health and economic impacts. A greater understanding of the fundamental neurochemistry that underlies healthy brain function, and the chemical pathways that manifest in brain damage or malfunction, are required to enable and accelerate therapeutic development. A previous limitation to the study of brain function and malfunction has been the limited number of techniques that provide both a wealth of biochemical information, and spatially resolved information (i.e., there was a previous lack of techniques that provided direct biochemical or elemental imaging at the cellular level). In recent times, a suite of direct spectroscopic imaging techniques, such as Fourier transform infrared spectroscopy (FTIR), X-ray fluorescence microscopy (XFM), and X-ray absorption spectroscopy (XAS) have been adapted, optimized and integrated into the field of neuroscience, to fill the above mentioned capability-gap. Advancements at synchrotron light sources, such as improved light intensity/flux, increased detector sensitivities and new capabilities of imaging/optics, has pushed the above suite of techniques beyond "proof-of-concept" studies, to routine application to study complex research problems in the field of neuroscience (and other scientific disciplines). This review examines several of the major advancements that have occurred over the last several years, with respect to FTIR, XFM and XAS capabilities at synchrotron facilities, and how the increases in technical capabilities have being integrated and used in the field of neuroscience.

Bone char vs. S-enriched bone char: Multi-method characterization of bone chars and their transformation in soil

To decrease environmental impacts from usage of mineral P fertilizers based on rock phosphate, alternative P fertilizers are urgently necessary but have to be critically evaluated for their characteristics and behaviour or effects in soil. For this reason, bone char (BC) and S-enriched BC (BC^plus), original and after one vegetation period in soil, were analysed by wet chemical analyses and XANES spectroscopy. According to X-ray absorption near edge structure (XANES) spectroscopy, both chars were dominated by P bound in hydroxyapatite, which was well reflected by wet chemical P fractionation, where Ca-P was the dominant fraction. Sulfur fractionation of both chars confirmed low percentages of sulfate-S according to XANES analysis but failed to detect elemental S in BC^plus. Because S concentrations in BC^plus were comparable to that of activated carbon used for biogas desulfurization and sorbed S was dominantly elemental S, BC seems to be well suited for biogas desulfurization. After one year in soil the disappearance of more easily soluble Ca(H₂PO₄)·2H₂O and strongly reduced proportions of sulfates and sulfonates in soil-BC^plus compared to BC^plus pointed to considerable advantages of BC^plus over BC. Taking into consideration the acidic pH of BC^plus, the high Ca, P, and S concentrations and the expected microbial induced "in situ digestion" of BC by oxidation of elemental S, it can be concluded that a cascade usage of BC as biogas adsorber and following subsequent usage of BC^plus as S/P/Ca/Mg (multi-element) fertilizer could be an alternative to mineral fertilizers based on rock phosphate. The agronomic efficiency and detailed application guidelines must be derived from established and currently running longer-term plot and field experiments.

Molecular speciation and transformation of soil legacy phosphorus with and without long-term phosphorus fertilization: Insights from bulk and microprobe spectroscopy

Soil legacy phosphorus (P) represents a substantial secondary P resource to postpone the global P crisis. To fully utilize this P reserve, the transformation of legacy P speciation in a black soil with and without P fertilization for 27 years was investigated by chemical fractionation, molecular-level bulk (P K-edge X-ray absorption near-edge, XANES; solution ³¹P nuclear magnetic resonance) and microprobe (µ-X-ray fluorescence and µ-XANES) spectroscopy. Results from both fractionation and P bulk-XANES concordantly indicated that Ca₂-P [Ca(H₂PO₄)₂] acts as a reserve of labile P in response to soils with or without P fertilization. Cropping for 27 years depleted hydroxyapatite while enriched iron-bound P in soils irrespective of P application. Similar accumulation of soil organic P (P_o), probably due to root residue inputs, occurred in both soils with and without P fertilization; the accumulated P_o was present as orthophosphate diesters in soils with P fertilization more than in soils without P fertilization, suggesting that the release of labile P_o was triggered by soil P deficits. These results provide vital information for agronomically and environmentally sustainable P management by demonstrating the potential crop availability of legacy soil P, which could reduce future P fertilization.