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Background: "Herbarium X-ray Fluorescence (XRF) Ionomics" is a new quantitative approach for extracting the elemental concentrations from herbarium specimens using handheld XRF devices. These instruments are principally designed for dense sample material of infinite thickness (such as rock or soil powder), and their built-in algorithms and factory calibrations perform poorly on the thin dry plant leaves encountered in herbaria. While empirical calibrations have been used for 'correcting' measured XRF values post hoc, this approach has major shortcomings. As such, a universal independent data analysis pipeline permitting full control and transparency throughout the quantification process is highly desirable. Here we have developed such a pipeline based on Dynamic Analysis as implemented in the GeoPIXE package, employing a Fundamental Parameters approach requiring only a description of the measurement hardware and derivation of the sample areal density, based on a universal standard., Results: The new pipeline was tested on potassium, calcium, manganese, iron, cobalt, nickel, and zinc concentrations in dry plant leaves. The Dynamic Analysis method can correct for complex X-ray interactions and performs better than both the built-in instrument algorithms and the empirical calibration approach. The new pipeline is also able to identify and quantify elements that are not detected and reported by the device built-in algorithms and provides good estimates of elemental concentrations where empirical calibrations are not straightforward., Conclusions: The new pipeline for processing XRF data of herbarium specimens has a greater accuracy and is more robust than the device built-in algorithms and empirical calibrations. It also gives access to all elements detected in the XRF spectrum. The new analysis pipeline has made Herbarium XRF approach even more powerful to study the metallome of existing plant collections., (© 2022. The Author(s).)

Copper (Cu) is one of the most harmful contaminants in fresh-water systems. Fish larvae such as sacfry are particularly vulnerable to metals such as copper (Cu) due to a less-developed excretory organ system and permeable skin that can absorb metals directly from the water. However, the sublethal effects of metals on this life stage are not well understood. This study assessed the sublethal toxicity of Cu on purple-spotted gudgeon sacfry (PSG, Mogurnda adspersa). For this purpose, 96 h Cu toxicity bioassays were performed and toxic effects of Cu on PSG were measured at different levels of biological organization, from the individual (loss of equilibrium, wet weight), to tissue (chemical changes in retinal tissue composition) and molecular responses (whole body amino acid (AA) profiles). The EC 10 and EC 50 (ECx: effect concentration that affected X% of test organisms) were found to be 12 (9 - 15) µg Cu L -1 and 22 (19 - 24) µg Cu L -1 , respectively. Copper stress caused a decrease in total amino acid content and changed the AA profile of PSG compared to the controls. Proton-induced X-ray emission (PIXE) mapping techniques showed accumulation of Cu in the retinal tissues disturbing the distribution of other elements such as zinc, sulfur, phosphorus and potassium. Fourier-transform infrared (FTIR) microspectroscopy of control and Cu treated eye tissues revealed a change in protein secondary structure in retinal tissues in response to Cu accumulation, as well as decreased levels of the molecular retinal, consistent with the degradation of rhodopsin, a key protein in the visual sensory system. This is the first study to demonstrate the multi-level responses of PSG arising from exposure to environmentally realistic Cu concentrations and suggests that AA profiling can serve as a useful tool to assess the impacts of metals on fresh-water organisms., (Copyright © 2022. Published by Elsevier B.V.)

Background: The fern Dicranopteris linearis is a hyperaccumulator of rare earth elements (REEs), aluminium (Al) and silicon (Si). However, the physiological mechanisms of tissue-level tolerance of high concentrations of REE and Al, and possible interactions with Si, are currently incompletely known., Methods: A particle-induced X-ray emission (μPIXE) microprobe with the Maia detector, scanning electron microscopy with energy-dispersive spectroscopy and chemical speciation modelling were used to decipher the localization and biochemistry of REEs, Al and Si in D. linearis during uptake, translocation and sequestration processes., Results: In the roots >80 % of REEs and Al were in apoplastic fractions, among which the REEs were most significantly co-localized with Si and phosphorus (P) in the epidermis. In the xylem sap, REEs were nearly 100 % present as REEH3SiO42+, without significant differences between the REEs, while 24-45 % of Al was present as Al-citrate and only 1.7-16 % Al was present as AlH3SiO42+. In the pinnules, REEs were mainly concentrated in necrotic lesions and in the epidermis, and REEs and Al were possibly co-deposited within phytoliths (SiO2). Different REEs had similar spatial localizations in the epidermis and exodermis of roots, the necrosis, veins and epidermis of pinnae of D. linearis., Conclusions: We posit that Si plays a critical role in REE and Al tolerance within the root apoplast, transport within the vascular bundle and sequestration within the blade of D. linearis., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The X-ray fluorescence microscopy (XFM) beamline is an in-vacuum undulator-based X-ray fluorescence (XRF) microprobe beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the 4-27 keV energy range, permitting K emission to Cd and L and M emission for all other heavier elements. With a practical low-energy detection cut-off of approximately 1.5 keV, low-Z detection is constrained to Si, with Al detectable under favourable circumstances. The beamline has two scanning stations: a Kirkpatrick-Baez mirror microprobe, which produces a focal spot of 2 µm × 2 µm FWHM, and a large-area scanning `milliprobe', which has the beam size defined by slits. Energy-dispersive detector systems include the Maia 384, Vortex-EM and Vortex-ME3 for XRF measurement, and the EIGER2 X 1 Mpixel array detector for scanning X-ray diffraction microscopy measurements. The beamline uses event-mode data acquisition that eliminates detector system time overheads, and motion control overheads are significantly reduced through the application of an efficient raster scanning algorithm. The minimal overheads, in conjunction with short dwell times per pixel, have allowed XFM to establish techniques such as full spectroscopic XANES fluorescence imaging, XRF tomography, fly scanning ptychography and high-definition XRF imaging over large areas. XFM provides diverse analysis capabilities in the fields of medicine, biology, geology, materials science and cultural heritage. This paper discusses the beamline status, scientific showcases and future upgrades.

Contents Summary 432 I. Introduction 433 II. Preparation of plant samples for X-ray micro-analysis 433 III. X-ray elemental mapping techniques 438 IV. X-ray data analysis 442 V. Case studies 443 VI. Conclusions 446 Acknowledgements 449 Author contributions 449 References 449 SUMMARY: Hyperaccumulators are attractive models for studying metal(loid) homeostasis, and probing the spatial distribution and coordination chemistry of metal(loid)s in their tissues is important for advancing our understanding of their ecophysiology. X-ray elemental mapping techniques are unique in providing in situ information, and with appropriate sample preparation offer results true to biological conditions of the living plant. The common platform of these techniques is a reliance on characteristic X-rays of elements present in a sample, excited either by electrons (scanning/transmission electron microscopy), protons (proton-induced X-ray emission) or X-rays (X-ray fluorescence microscopy). Elucidating the cellular and tissue-level distribution of metal(loid)s is inherently challenging and accurate X-ray analysis places strict demands on sample collection, preparation and analytical conditions, to avoid elemental redistribution, chemical modification or ultrastructural alterations. We compare the merits and limitations of the individual techniques, and focus on the optimal field of applications for inferring ecophysiological processes in hyperaccumulator plants. X-ray elemental mapping techniques can play a key role in answering questions at every level of metal(loid) homeostasis in plants, from the rhizosphere interface, to uptake pathways in the roots and shoots. Further improvements in technological capabilities offer exciting perspectives for the study of hyperaccumulator plants into the future., (© 2017 University of Queensland. New Phytologist © 2017 New Phytologist Trust.)

• Accumulation of arsenic (As) within plant tissues represents a human health risk, but there remains much to learn regarding the speciation of As within plants. • We developed synchrotron-based fluorescence-X-ray absorption near-edge spectroscopy (fluorescence-XANES) imaging in hydrated and fresh plant tissues to provide laterally resolved data on the in situ speciation of As in roots of wheat (Triticum aestivum) and rice (Oryza sativa) exposed to 2 μM As(V) or As(III). • When exposed to As(V), the As was rapidly reduced to As(III) within the root, with As(V) calculated to be present only in the rhizodermis. However, no uncomplexed As(III) was detected in any root tissues, because of the efficient formation of the As(III)-thiol complex - this As species was calculated to account for all of the As in the cortex and stele. The observation that uncomplexed As(III) was below the detection limit in all root tissues explains why the transport of As to the shoots is low, given that uncomplexed As(III) is the major As species transported within the xylem and phloem. • Using fluorescence-XANES imaging, we have provided in situ data showing the accumulation and transformation of As within hydrated and fresh root tissues., (© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.)

Many metals and metalloids, jointly termed metal(loid)s, are toxic to plants even at low levels. This has limited the study of their uptake, distribution, and modes of action in plant roots grown at physiologically relevant concentrations. Synchrotron-based X-ray fluorescence microscopy was used to examine metal(loid)s in hydrated cowpea (Vigna unguiculata L.) roots exposed to Zn(II), Ni(II), Mn(II), Cu(II), Hg(II), Se(IV), Se(VI), As(III), or As(V). Development of a mathematical model enabled in situ quantitative determination of their distribution in root tissues. The binding strength of metals influenced the extent of their movement through the root cylinder, which influenced the toxic effects exerted-metals (e.g. Cu, Hg) that bind more strongly to hard ligands had high concentrations in the rhizodermis and caused this tissue to rupture, while other metals (e.g. Ni, Zn) moved further into the root cylinder and did not cause ruptures. When longitudinal distributions were examined, the highest Se concentration in roots exposed to Se(VI) was in the more proximal root tissues, suggesting that Se(VI) is readily loaded into the stele. This contrasted with other metal(loid)s (e.g. Mn, As), which accumulated in the apex. These differences in metal(loid) spatial distribution provide valuable quantitative data on metal(loid) physiology, including uptake, transport, and toxicity in plant roots., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Determining the chemical and biological compositions of the tumour models used in pharmacological studies is crucial for understanding the interactions between the drug molecules and the tumour micro-environment. Conventional techniques for spheroid characterisation require intensive chemical pre-treatments that result in the removal of unbound metabolites. In this study, the spectroscopic techniques, scanning transmission ion microscopy (STIM), proton-induced X-ray emission (PIXE) mapping, scanning X-ray fluorescence microscopy (SXFM), and Fourier transform infrared (FT-IR) imaging were employed to gain complementary information on the compositions of untreated DLD-l cancer cell spheroids. When used together, these techniques exhibited great potential for providing a comprehensive over-view of the density, biochemistry and elemental compositions within the different regions of the spheroids. STIM density and elemental maps correlated well with cellular density across the spheroid, and showed the accumulation of S, Cu and various lighter elements in the necrotic region. High levels of oxidative stress were evident in the hypoxic region, and different degrees of cellular necrosis as well as high levels of lactate and collagen within the necrotic region were suggested by FT-IR markers. FT-IR imaging was further employed to study the pharmacodynamics of known the cytotoxins, cisplatin and Pt1C3. Cisplatin was observed to induce minimal biochemical changes to the spheroids following 24 hour incubations, whereas Pt1C3 caused severe cellular damage to the spheroid periphery; consistent with their different modes of action.

A historical self-portrait painted by Sir Arthur Streeton (1867-1943) has been studied with fast-scanning X-ray fluorescence microscopy using synchrotron radiation. One of the technique's unique strengths is the ability to reveal metal distributions in the pigments of underlying brushstrokes, thus providing information critical to the interpretation of a painting. We have applied the nondestructive technique with the event-mode Maia X-ray detector, which has the capability to record elemental maps at megapixels per hour with the full X-ray fluorescence spectrum collected per pixel. The painting poses a difficult challenge to conventional X-ray analysis, because it was completely obscured with heavy brushstrokes of highly X-ray absorptive lead white paint (2PbCO(3)·Pb(OH)(2)) by the artist, making it an excellent candidate for the application of the synchrotron-based technique. The 25 megapixel elemental maps were successfully observed through the lead white paint across the 200 × 300 mm(2) scan area. The sweeping brushstrokes of the lead white overpaint contributed significant detrimental structure to the elemental maps. A corrective procedure was devised to enhance the visualization of the elemental maps by using the elastic X-ray scatter as a proxy for the lead white overpaint. We foresee the technique applied to the most demanding of culturally significant artworks where conventional analytical methods are inadequate.

X-ray fluorescence microscopy (XFM) facilitates high-sensitivity quantitative imaging of trace metals at high spatial resolution over large sample areas and can be applied to a diverse range of biological samples. Accurate determination of elemental content from recorded spectra requires proper calibration of the XFM instrument under the relevant operating conditions. Here, we describe the manufacture, characterization, and utilization of multi-element thin-film reference foils for use in calibration of XFM measurements of biological and other specimens. We have used these internal standards to assess the two-dimensional distribution of trace metals in a thin tissue section of a rat hippocampus. The data used in this study was acquired at the XFM beamline of the Australian Synchrotron using a new 384-element array detector (Maia) and at beamline 2-ID-E at the Advanced Photon Source. Post-processing of samples by different fixation techniques was investigated, with the conclusion that differences in solvent type and sample handling can significantly alter elemental content. The present study highlights the quantitative capability, high statistical power, and versatility of the XFM technique for mapping trace metals in biological samples, e.g., brain tissue samples in order to help understand neurological processes, especially when implemented in conjunction with a high-performance detector such as Maia.

The phytotoxicity of trace metals is of global concern due to contamination of the landscape by human activities. Using synchrotron-based x-ray fluorescence microscopy and x-ray absorption spectroscopy, the distribution and speciation of copper (Cu), nickel (Ni), and zinc (Zn) was examined in situ using hydrated roots of cowpea (Vigna unguiculata) exposed to 1.5 μm Cu, 5 μm Ni, or 40 μm Zn for 1 to 24 h. After 24 h of exposure, most Cu was bound to polygalacturonic acid of the rhizodermis and outer cortex, suggesting that binding of Cu to walls of cells in the rhizodermis possibly contributes to the toxic effects of Cu. When exposed to Zn, cortical concentrations remained comparatively low with much of the Zn accumulating in the meristematic region and moving into the stele; approximately 60% to 85% of the total Zn stored as Zn phytate within 3 h of exposure. While Ni concentrations were high in both the cortex and meristem, concentrations in the stele were comparatively low. To our knowledge, this is the first report of the in situ distribution and speciation of Cu, Ni, and Zn in hydrated (and fresh) plant tissues, providing valuable information on the potential mechanisms by which they are toxic.

The aim of this study was to determine specific distribution of metals in the termite Tumulitermes tumuli (Froggatt) and identify specific organs within the termite that host elevated metals and therefore play an important role in the regulation and transfer of these back into the environment. Like other insects, termites bio-accumulate essential metals to reinforce cuticular structures and utilize storage detoxification for other metals including Ca, P, Mg and K. Previously, Mn and Zn have been found concentrated in mandible tips and are associated with increased hardness whereas Ca, P, Mg and K are accumulated in Malpighian tubules. Using high resolution Particle Induced X-Ray Emission (PIXE) mapping of whole termites and Scanning Electron Microscope (SEM) Energy Dispersive X-ray (EDX) spot analysis, localised accumulations of metals in the termite T. tumuli were identified. Tumulitermes tumuli was found to have proportionally high Mn concentrations in mandible tips. Malpighian tubules had significant enrichment of Zn (1.6%), Mg (4.9%), P (6.8%), Ca (2.7%) and K (2.4%). Synchrotron scanning X-ray Fluorescence Microprobe (XFM) mapping demonstrated two different concretion types defined by the mutually exclusive presence of Ca and Zn. In-situ SEM EDX realisation of these concretions is problematic due to the excitation volume caused by operating conditions required to detect minor amounts of Zn in the presence of significant amounts of Na. For this reason, previous researchers have not demonstrated this surprising finding.

Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples.

The development of analytical techniques for the measurement of trace elements in cellular compartments of developing teeth remains an important methodological issue in dental research. Recent advances in third generation synchrotron facilities have provided high brilliance X-ray sources that can be effectively used to study trace element distributions in small spatial regions with low detection limits. The present study describes for the first time the application of synchrotron radiation induced X-ray emission (SRIXE) in measuring the distribution of zinc and lead in the ameloblasts of developing Wistar rat teeth. Wistar rats were fed a standard rat diet, containing the normal dietary requirements of zinc, ad libitum and exposed to 100 ppm of lead in drinking water. Resin embedded sections of first mandibular molars were analysed using a 13.3 keV incident monochromatic X-ray beam focussed to a 0.2 microm spot. Characteristic X-rays arising from the entire thickness of the sample were measured using an energy dispersive detector for quantitative analysis of elemental concentrations. The results showed that intranuclear concentrations of zinc were greater than levels in the cytoplasm. Furthermore, nuclear and cytoplasmic concentrations of zinc in the maturation stage (742+/-27 and 424+/-25 ppm, respectively) were significantly higher than the zinc levels observed in the nucleus and cytoplasm of presecretory stage ameloblasts (132+/-10 and 109+/-10 ppm, respectively) (p<0.05). A clear lead signal above the background was not detected in the ameloblasts and lead concentrations could only be reliably measured in the developing enamel. Overall, SRIXE was an effective method of studying the spatial distribution of zinc in the cells of developing teeth and offered a unique combination of sub-micron spatial resolution and parts-per-million detection limits (0.8-1 and 0.6-1 ppm for zinc and lead, respectively).

Lead is one of the most hazardous environmental toxins known. The assessment of lead in dental hard tissues is important in the understanding of its toxic effects on oral tissues and in estimating exposure and body burden in individuals exposed to lead from the environment. However, current information on the uptake and distribution of lead in enamel and dentine is limited. The aim of this project was to study, at high resolution, the spatial distribution of lead in enamel and coronal dentine using an experimental rat model. A dose of 40 mg/L of lead nitrate was administered to pregnant female rats during the periods of gestation and lactation through drinking water. First mandibular molar teeth were removed from their 15-d-old pups and the distribution of lead was studied using a nuclear microprobe (NMP). The distribution of lead in enamel and coronal dentine showed four distinct zones with significantly different mean lead concentrations (p<0.05). High levels of lead were observed in the superficial regions of enamel and in the dentine directly adjacent to the pulp. Additionally, the results confirmed that the NMP is capable of mapping the distribution of lead in teeth at micron resolutions with a detection limit of approx 1 microg/g.

At a porphyry copper-gold deposit in Bajo de la Alumbrera, Argentina, silicate-melt inclusions coexist with hypersaline liquid- and vapor-rich inclusions in the earliest magmatic-hydrothermal quartz veins. Copper concentrations of the hypersaline liquid and vapor inclusions reached maxima of 10.0 weight % (wt %) and 4.5 wt %, respectively. These unusually copper-rich inclusions are considered to be the most primitive ore fluid found thus far. Their preservation with coexisting melt allows for the direct quantification of important oreforming processes, including determination of bulk partition coefficients of metals from magma into ore-forming magmatic volatile phases.