X-ray fluorescence analysis using synchrotron radiation at the photon factory

X-ray fluorescence experiments at the Photon Factory in Japan are described. An energy-dispersive X-ray fluorescence system was combined with various excitation modes, i.e., a continuum and a monochromatic excitation, which consist of a crystal monochromator or a wide band pass monochromator. These excitation modes provide a wide range of band width and photon flux of excitation beams. Minimum detection limits obtained for a thin sample were less than 0.1 ppm and 0.1 pg when there was no line interference. Advantages of using monochromatic excitation are discussed, with emphasis on the possibility of chemical state analysis. Grazing incidence X-ray fluorescence is a technique very appropriate to synchrotron radiation characteristics. Near-surface analysis and trace analysis of solution samples placed on a total reflection support were made. Future plans are discussed, including microbeam analysis, tomography, X-ray excited optical fluorescence, and applications of insertion devices (undulator and wiggler).     

Using synchrotron X-ray fluorescence microprobes in the study of metal homeostasis in plants

Background and Aims

This Botanical Briefing reviews the application of synchrotron X-ray fluorescence (SXRF) microprobes to the plant sciences; how the technique has expanded our knowledge of metal(loid) homeostasis, and how it can be used in the future.

Scope

The use of SXRF microspectroscopy and microtomography in research on metal homeostasis in plants is reviewed. The potential use of SXRF as part of the ionomics toolbox, where it is able to provide fundamental information on the way that plants control metal homeostasis, is recommended.

Conclusions

SXRF is one of the few techniques capable of providing spatially resolved in-vivo metal abundance data on a sub-micrometre scale, without the need for chemical fixation, coating, drying or even sectioning of samples. This gives researchers the ability to uncover mechanisms of plant metal homeostasis that can potentially be obscured by the artefacts of sample preparation. Further, new generation synchrotrons with smaller beam sizes and more sensitive detection systems will allow for the imaging of metal distribution within single living plant cells. Even greater advances in our understanding of metal homeostasis in plants can be gained by overcoming some of the practical boundaries that exist in the use of SXRF analysis.Key words: Metal homeostasis, synchrotron X-ray fluorescence, SXRF, microspectroscopy, microtomography, X-ray absorption spectroscopy, XAS, ionomics, Arabidopsis thaliana, hyperaccumulator     

X-ray spectroscopy and imaging of selenium in living systems

Background

Selenium is an essential element with a rich and varied chemistry in living organisms. It plays a variety of important roles ranging from being essential in enzymes that are critical for redox homeostasis to acting as a deterrent for herbivory in hyperaccumulating plants. Despite its importance there are many open questions, especially related to its chemistry in situ within living organisms.

Molybdenum X-ray absorption edges from 200 to 20,000 eV: The benefits of soft X-ray spectroscopy for chemical speciation

We have surveyed the chemical utility of the near-edge structure of molybdenum X-ray absorption edges from the hard X-ray K-edge at 20,000 eV down to the soft X-ray M_4,5-edges at ∼230 eV. We compared, for each edge, the spectra of two tetrahedral anions, and . We used three criteria for assessing near-edge structure of each edge: (i) the ratio of the observed chemical shift between and and the linewidth, (ii) the chemical information from analysis of the near-edge structure and (iii) the ease of measurement using fluorescence detection. Not surprisingly, the K-edge was by far the easiest to measure, but it contained the least information. The L_2,3-edges, although harder to measure, had benefits with regard to selection rules and chemical speciation in that they had both a greater chemical shift as well as detailed lineshapes which could be theoretically analyzed in terms of Mo ligand field, symmetry, and covalency. The soft X-ray M_2,3-edges were perhaps the least useful, in that they were difficult to measure using fluorescence detection and had very similar information content to the corresponding L_2,3-edges.Interestingly, the soft X-ray, low energy (∼230 eV) M_4,5-edges had greatest potential chemical sensitivity and using our high-resolution superconducting tunnel junction (STJ) fluorescence detector they appear to be straightforward to measure. The spectra were amenable to analysis using both the TT-multiplet approach and FEFF. The results using FEFF indicate that the sharp near-edge peaks arise from 3d → 5p transitions, while the broad edge structure has predominately 3d → 4f character. A proper understanding of the dependence of these soft X-ray spectra on ligand field and site geometry is necessary before a complete assessment of the utility of the Mo M_4,5-edges can be made. This work includes crystallographic characterization of sodium tetrathiomolybdate.     

Biomedical applications of photon-induced X-ray fluorescence

An X-ray fluorescence method for in vitro analysis of trace elements is presented. The method is characterized by the use of an X-ray tube with secondary targets as a quasimonoenergetic radiation source, and by “infinitely thin” specimens. Different aspects have been examined in order to optimize the sensitivity of the method. It is extremely important to use secondary targets as pure as possible and collimators internally covered by the same element as the secondary target. It is also important to reduce the contribution at the XRF spectrum of photons scattered by the sample, by the sample support, and by the air. Preconcentration techniques can conveniently also be used to this purpose. In this work, biological samples are preconcentrated by reducing them to ash. Typical sensitivities obtained are in the order of 1–5 ng/cm² in a counting time of 10³ s for elements with atomic number ranging from 24 (chromium) to 40 (zirconium).     

BMIT facility at the Canadian Light Source: Advances in X-ray phase-sensitive imaging

The BioMedical Imaging and Therapy (BMIT) facility [1,2] located at the Canadian Light Source, provides synchrotron-specific imaging and radiation therapy capabilities. There are two separate beamlines used for experiments: the bending magnet (05B1-1) and the insertion device (05ID-2) beamline.The bending magnet beamline provides access to monochromatic beam spanning a spectral range of 15–40 keV, and the beam is 240 mm wide in the POE-2 experimental hutch. Users can also perform experiments with polychromatic (pink) beam.The insertion device beamline was officially opened for general user program in 2015. The source for the ID beamline is a multi-pole, superconducting 4.3 T wiggler. The high field gives a critical energy over 20 keV. The optics hutches prepare a beam that is 220 mm wide in the last experimental hutch SOE-1. The monochromatic spectral range spans 25–150+ keV. Several different X-ray detectors are available for both beamlines, with resolutions ranging from 2 μm to 200 μm.BMIT provides a number of imaging techniques including standard absorption X-ray imaging, K-edge subtraction imaging (KES), in-line phase contrast imaging (also known as propagation based imaging, PBI) and Diffraction Enhanced Imaging/Analyzer Based Imaging (DEI/ABI), all in either projection or CT mode. PBI and DEI/ABI are particularly important tools for BMIT users since these techniques enable visualization of soft tissue and allow for low dose imaging.     

Accuracy of predicting chemical body composition of growing pigs using dual-energy X-ray absorptiometry

Studies in animal science assessing nutrient and energy efficiency or determining nutrient requirements benefit from gathering exact measurements of body composition or body nutrient contents. Those are acquired by standardized dissection or by grinding the body followed by wet chemical analysis, respectively. The two methods do not result in the same type of information, but both are destructive. Harnessing human medical imaging techniques for animal science can enable repeated measurements of individuals over time and reduce the number of individuals required for research. Among imaging techniques, dual-energy X-ray absorptiometry (DXA) is particularly promising. However, the measurements obtained with DXA do not perfectly match dissections or chemical analyses, requiring the adjustment of the DXA via calibration equations. Several calibration regressions have been published, but comparative studies of those regression equations and whether they are applicable to different data sets are pending. Thus, it is currently not clear whether existing regression equations can be directly used to convert DXA measurements into chemical values or whether each individual DXA device will require its own calibration. Our study builds prediction equations that relate body composition to the content of single nutrients in growing entire male pigs (BW range 20–100 kg) as determined by both DXA and chemical analyses, with R² ranging between 0.89 for ash and 0.99 for water and CP. Moreover, we show that the chemical composition of the empty body can be satisfactorily determined by DXA scans of carcasses, with the prediction error ranging between 4.3% for CP and 12.6% for ash. Finally, we compare existing prediction equations for pigs of a similar range of BWs with the equations derived from our DXA measurements and evaluate their fit with our chemical analysis data. We found that existing equations for absolute contents that were built using the same DXA beam technology predicted our data more precisely than equations based on different technologies and percentages of fat and lean mass. This indicates that the creation of generic regression equations that yield reliable estimates of body composition in pigs of different growth stages, sexes and genetic breeds could be achievable in the near future. DXA may be a promising tool for high-throughput phenotyping for genetic studies, because it efficiently measures body composition in a large number and wide array of animals.     

Multimodal Imaging and Soft X-Ray Tomography of Fluorescent Nanodiamonds in Cancer Cells

Multimodal imaging promises to revolutionize the understanding of biological processes across scales in space and time by combining the strengths of multiple imaging techniques. Fluorescent nanodiamonds (FNDs) are biocompatible, chemically inert, provide high contrast in light- and electron-based microscopy, and are versatile optical quantum sensors. Here it is demonstrated that FNDs also provide high absorption contrast in nanoscale 3D soft X-ray tomograms with a resolution of 28 nm in all dimensions. Confocal fluorescence, atomic force, and scanning electron microscopy images of FNDs inside and on the surface of PC3 cancer cells with sub-micrometer precision are correlated. FNDs are found inside ≈1 µm sized vesicles present in the cytoplasm, providing direct evidence of the active uptake of bare FNDs by cancer cells. Imaging artefacts are quantified and separated from changes in cell morphology caused by sample preparation. These results demonstrate the utility of FNDs in multimodal imaging, contribute to the understanding of the fate of FNDs in cells, and open up new possibilities for biological imaging and sensing across the nano- and microscale.     

X-ray microtomography for imaging of developing spiders inside egg cocoons

Embryogenesis is especially sensitive to external factors. The changes in its course are often used as biomarkers of environmental impact. Since spider embryogenesis takes place inside cocoons, it is crucial to find a reliable tool to analyze this developmental phase with no intrusion into the cocoons. The aim of this study was to verify the efficacy of X-ray microtomography for non-invasive analysis of embryonic morphology and egg quantity in the cocoons of Xerolycosa nemoralis and Agelena labyrinthica from polluted and reference sites. X-ray microtomography slice images as well as 3D images and animations obtained from digital visualization of those slides were used to study the morphology of embryos and egg arrangement in the cocoons. Any disorders in embryogenesis or malformation of embryos in relation to site of origin have not been found, but inside an egg cocoon of X. nemoralis from the polluted site embryos differing form each other by one developmental stage were identified. Egg calculation revealed a K- reproductive strategy of X. nemoralis from polluted sites. Finally, future prospects and benefits, and weaknessess of this method for the study of spider cocoons have presented.     

X-ray microanalysis of black piedra

The elements present in the fungal structures produced by Piedraia hortae in vivo and in vitro have been investigated using electron microscopy X-ray microanalysis. Phosphorus, sulphur and calcium were detected in the nodules which developed on hair and on colonies on culture. These elements belong to the extracellular material that compacts the pseudoparenchymatous organization of the fungus. They may be present due to the capacity of melanin-like pigments to sequester ions and/or they may form part of the sulphates and phosphates of the polyanionic mucopolysaccharides that constitute the extracellular material. Environmental contaminants such as aluminium, silicon and iron were detected exclusively on the surface of the nodule. They were deposited or linked to the residual molecules produced during the breakdown of the cuticular keratin. The advantages of these techniques for elucidating the chemical nature of fungal structures are discussed.     

High-resolution structure of the photosynthetic Mn4Ca catalyst from X-ray spectroscopy

The application of high-resolution X-ray spectroscopy methods to study the photosynthetic water oxidizing complex, which contains a unique hetero-nuclear catalytic Mn4Ca cluster, is described. Issues of X-ray damage, especially at the metal sites in the Mn4Ca cluster, are discussed. The structure of the Mn4Ca catalyst at high resolution, which has so far eluded attempts of determination by X-ray diffraction, X-ray absorption fine structure (EXAFS) and other spectroscopic techniques, has been addressed using polarized EXAFS techniques applied to oriented photosystem II (PSII) membrane preparations and PSII single crystals. A review of how the resolution of traditional EXAFS techniques can be improved, using methods such as range-extended EXAFS, is presented, and the changes that occur in the structure of the cluster as it advances through the catalytic cycle are described. X-ray absorption and emission techniques (XANES and Kbeta emission) have been used earlier to determine the oxidation states of the Mn4Ca cluster, and in this report we review the use of X-ray resonant Raman spectroscopy to understand the electronic structure of the Mn4Ca cluster as it cycles through the intermediate S-states.     

Transmission photoemission electron microscopy for lateral mapping of the X-ray absorption structure of a metalloprotein in a liquid cell

We use photoemission electron microscopy in an X-ray transmission mode for full-field imaging of the X-ray absorption structure of copper in the respiratory metalloprotein hemocyanin KLH1. It contains 160 oxygen binding sites. Each site reversibly binds one molecule oxygen between two copper atoms. In our setup, hemocyanin is dissolved in aqueous solution and enclosed in an ultra-high vacuum compatible liquid sample cell with silicon nitride membranes. The local X-ray absorption structure of the liquid sample is converted into photoelectrons at the microscope side of the cell acting as a photocathode. In this way, different copper valencies are laterally distinguished under in vivo-like conditions, attributed to Cu(I) in the deoxy-state and Cu(II) in the oxy-state.     

Determination of ruthenium on DNA by XRF

An X-ray fluorescence (XRF) technique is used to quantitate the binding of [H₂O(NH₃)₅Ru^II]²⁺ to DNA. This method is shown to be more sensitive, precise, and convenient than conventional optical absorption (OA) spectroscopy, differential pulse voltammetry (DPV), or atomic absorption (AA) techniques. X-ray fluorescence is insensitive to the oxidation state or coordination environment of Ru and so can be used to determine total Ru. The minimum detectable amount of Ru is 10 ng in 1 h of counting time, using a 100-mCi¹²⁵I source. The specific advantages of the XRF method over the conventional methods are outlined.     

Seed viability of five wild Saudi Arabian species by germination and X-ray tests

Our objective was to evaluate the usefulness of the germination vs. the X-ray test in determining the initial viability of seeds of five wild species (Moringa peregrina, Abrus precatorius, Arthrocnemum macrostachyum, Acacia ehrenbergiana and Acacia tortilis) from Saudi Arabia. Usually several days were required to determine the viability of all five species via germination tests. However, X-ray test will give immediate results on filled/viable seeds. Seeds of all species, except Acacia ehrenbergiana and Acacia tortilis showed high viability in both germination (96–72% at 25/15 °C, 94–70% at 35/25 °C) and X-ray (100–80%) test. Furthermore, there was a general agreement between the germination (19%, 14% at 25/15 °C and 17% and 12% at 35/25 °C) and X-ray (8%, 4%) tests in which seed viability of Acacia ehrenbergiana and Acacia tortilis was very low due to insect damaged embryo as shown in X-ray analysis. Seeds of Abruspreca torius have physical dormancy, which was broken by scarification in concentrated sulfuric acid (10 min), and they exhibited high viability in both the germination (83% at 25/15 °C and 81% at 35/25 °C) and X-ray (96%) tests. Most of the nongerminated seeds of the five species except those of Acacia ehrenbergiana and Acacia tortilis, were alive as judged by the tetrazolium test (TZ). Thus, for the five species examined, the X-ray test was proved to be a good and rapid predictor of seed viability.     

Determination of seed viability of eight wild Saudi Arabian species by germination and X-ray tests

Our purpose was to evaluate the usefulness of the germination vs. the X-ray test in determining the initial viability of seeds of eight wild species (Salvia spinosa, Salvia aegyptiaca, Ochradenus baccatus, Ochradenus arabicus, Suaeda aegyptiaca, Suaeda vermiculata, Prosopisfarcta and Panicumturgidum) from Saudi Arabia. Several days were required to determine viability of all eight species via germination tests, while immediate results on filled/viable seeds were obtained with the X-ray test. Seeds of all the species, except Sa.aegyptiaca, showed high viability in both the germination (98–70% at 25/15 °C, 93–66% at 35/25 °C) and X-ray (100–75%) test. Furthermore, there was general agreement between the germination (10% at 25/15 °C and 8% at 35/25 °C) and X-ray (5%) tests that seed viability of Sa.aegyptiaca was very low, and X-ray analysis revealed that this was due to poor embryo development. Seeds of P.farcta have physical dormancy, which was broken by scarification in concentrated sulfuric acid (10 min), and they exhibited high viability in both the germination (98% at 25/15 °C and 93% at 35/25 °C) and X-ray (98%) test. Most of the nongerminated seeds of the eight species except those of Sa.aegyptiaca were alive as judged by the tetrazolium test (TZ). Thus, for the eight species examined, the X-ray test was a good and rapid predictor of seed viability.     

Analysis of sulfur biochemistry of sulfur bacteria using X-ray absorption spectroscopy.

Many sulfide-oxidizing organisms, including the photosynthetic sulfur bacteria, store sulfur in "sulfur globules" that are readily detected microscopically. The chemical form of sulfur in these globules is currently the focus of a debate, because they have been described as "liquid" by some observers, although no known allotrope of sulfur is liquid at physiological temperatures. In the present work we have used sulfur K-edge X-ray absorption spectroscopy to identify and quantify the chemical forms of sulfur in a variety of bacterial cells, including photosynthetic sulfur bacteria. We have also taken advantage of X-ray fluorescence self-absorption to derive estimates of the size and density of the sulfur globules in photosynthetic bacteria. We find that the form of sulfur that most resembles the globule sulfur is simply solid S(8), rather than more exotic forms previously proposed.     

Dynamic motions of ice-binding proteins in living Caenorhabditis elegans using diffracted X-ray blinking and tracking

The dynamic properties of protein molecules are involved in the relationship between their structure and function. Time-resolved X-ray observation enables capturing the structures of biomolecules with picometre-scale precision. However, this technique has yet to be implemented in living animals. Here, we examined diffracted X-ray blinking (DXB) and diffracted X-ray tracking (DXT) to observe the dynamics of a protein located on intestinal cells in adult Caenorhabditis elegans. This in vivo tissue-specific DXB was examined at temperatures from 20 °C to ?10 °C for a recombinant ice-binding protein from Antarctomyces psychrotrophicus (AnpIBP) connected with the cells through a transmembrane CD4 protein equipped with a glycine-serine linker. AnpIBP inhibits ice growth at subzero temperatures by binding to ice crystals. We found that the rotational motion of AnpIBP decreases at ?10 °C. In contrast, the motion of the AnpIBP mutant, which has a defective ice-binding ability, did not decrease at ?10 °C. The twisting and tilting motional speeds of AnpIBPs measured above 5 °C by DXT were always higher than those of the defective AnpIBP mutant. These results suggest that wild-type AnpIBP is highly mobile in solution, and it is halted at subzero temperatures through ice binding. DXB and DXT allow for exploring protein behaviour in live animals with subnano resolution precision.     

Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography

With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.     

In situ analysis of metal(loid)s in plants: State of the art and artefacts

Metals and metalloids play important roles in plant function and metabolism. Likewise, plants subsequently introduce vital dietary nutrition to people and animals. Understanding the transport, localisation and speciation of these elements is critical for understanding availability and metabolic pathways. Subsequently this knowledge can be applied to plant physiology and agricultural research, food science and genetic engineering.This review focuses on the most recent status of in situ techniques to visualise spatial distributions and assess the speciation of metals and metalloids. The techniques addressed include: histochemical analysis, autoradiography, LA-ICP-MS, SIMS, SEM including EDX, PIXE; and synchrotron methods: XRF, differential and fluorescence tomography, and X-ray absorption techniques.This review has been written with the intent of plant researchers to gain familiarity with techniques to which they are not accustom but wish to extend their research with alternative, but complementary, capabilities. Importantly, the disadvantages as well as advantages, have been highlighted for each technique and potential artefacts induced by the analysis or sample preparation are reviewed. These often overlooked aspects are the points critical for novice use of unfamiliar techniques and are offered for advancing research approaches commensurate with the accelerating interest regarding metal(loid)s in botanical specimens.     

Revisiting the localisation of Zn cations sorbed on pathological apatite calcifications made through X-ray absorption spectroscopy

The role of oligo-elements such as Zn in the genesis of pathological calcifications is widely debated in the literature. An essential element of discussion is given by their localisation either at the surface or within the Ca apatite crystalline network. To determine the localisation, X-ray absorption experiments have been performed at SOLEIL. The Exafs results suggest that Zn atoms, present in the Zn²⁺ form, are bound to about 4 O atoms at a distance of 2.00 Å, while the interatomic distance R_CaO ranges between 2.35 Å and 2.71 Å. Taking into account the content of Zn (around 1000 ppm) and the difference in ionic radius between Zn²⁺ (0.074 nm) and Ca²⁺ (0.099 nm), a significant longer interatomic distance would be expected in the case of Zn replacing Ca within the apatite crystalline network. We thus conclude that Zn atoms are localised at the surface and not in the apatite nanocrystal structure. Such structural result has essential biological implications for at least two reasons. Some oligoelements have a marked effect on the transformation of chemical phases, and may modify the morphology of crystals. These are both major issues because, in the case of kidney stones, the medical treatment depends strongly on the precise chemical phase and on the morphology of the biological entities at both macroscopic and mesoscopic scales.