The role of plants in ironstone evolution: iron and aluminium cycling in the rhizosphere

The Carajás plateaus in Brazil host endemic epilithic vegetation ("campo rupestre") on top of ironstone duricrusts, known as canga. This capping rock is primarily composed of iron(III) oxide minerals and forms a physically resistant horizon. Field observations reveal an intimate interaction between canga's surface and two native sedges (Rhynchospora barbata and Bulbostylis cangae). These observations suggest that certain plants contribute to the biogeochemical cycling of iron. Iron dissolution features at the root-rock interface were characterised using synchrotron-based techniques, Raman spectroscopy and scanning electron microscopy. These microscale characterisations indicate that iron is preferentially leached in the rhizosphere, enriching the comparatively insoluble aluminium around root channels. Oxalic acid and other exudates were detected in active root channels, signifying ligand-controlled iron oxide dissolution, likely driven by the plants' requirements for goethite-associated nutrients such as phosphorus. The excess iron not uptaken by the plant can reprecipitate in and around roots, line root channels and cement detrital fragments in the soil crust at the base of the plants. The reprecipitation of iron is significant as it provides a continuously forming cement, which makes canga horizons a 'self-healing' cover and contributes to them being the world's most stable continuously exposed land surfaces. Aluminium hydroxide precipitates ("gibbsite cutans") were also detected, coating some of the root cavities, often in alternating layers with goethite. This alternating pattern may correspond with oscillating oxygen concentrations in the rhizosphere. Microbial lineages known to contain iron-reducing bacteria were identified in the sedge rhizospheric microbiome and likely contribute to the reductive dissolution of iron(III) oxides within canga. Drying or percolation of oxygenated water to these anaerobic niches have led to iron mineralisation of biofilms, detected in many root channels. This study sheds light on plants' direct and indirect involvement in canga evolution, with possible implications for revegetation and surface restoration of iron mine sites.

Operando Investigation of Silicon Anodes During Electrochemical Cycling in Li-ion Batteries

Silicon (Si) is recognized as a promising anode material for next-generation anodes due to its high capacity. However, large volume expansion and active particle pulverization during cycling rapidly deteriorate the battery performance. The relationship between Si anode particle size and particle pulverization, and the structure evolution of Si particles during cycling is not well understood. In this study, a quantitative, time-resolved "operando" small angle X-ray scattering (SAXS) investigation into the morphological change of unwrapped and reduced graphene oxide (rGO) wrapped Si nanoparticles (Si@rGO) is conducted with respect to the operating voltage. The results provide a clear picture of Si particle size change and the role of nonrigid rGO in mitigating Si volume expansion and pulverization. Further, this study demonstrates the advantage of "operando" SAXS in electrochemical environments as compared to other approaches.

Accelerating bioleaching of tungsten mining wastes using indigenous acidophilic bacteria

The growing amount of W mining waste produced globally is of concern for its proven hazard to the environment and to human health. While uncontrolled biooxidation can result in environmental harm, bioleaching, where pregnant leach solutions are controlled, has been widely used in the mining industry for valuable metals recovery, often from low-grade materials. This bioleaching study was developed to evaluate whether the biogeochemical reprocessing of W tailings could be employed for the decontamination of W-bearing mine waste, combined with valuable metals recovery, i.e., turning a waste into a resource. Using an in-vitro laboratory model, the susceptibility of wolframite [(Fe,Mn)WO₄] to acid dissolution during the concomitant oxidation of co-localized sulfidic minerals represented the basic strategy for enhanced W recovery. Encouragingly, geochemistry and synchrotron-based X-ray absorption near edge structure of weathered W tailings demonstrated that early-stage wolframite dissolution occurred. However, W dissolution was limited by the formation of secondary W minerals; weathering produced two secondary W minerals i.e., gallium-rich tungstate and minor sanmartinite [(Zn,Fe)WO₄]. The dissolution and re-precipitation of W minerals may provide a strategy for W waste reprocessing if the two processes can be separated by initially putting W into solution, and allowing for its extraction from tailings, followed by its' recovery by secondary W mineral formation.

Spatial distribution of elements during osteoarthritis disease progression using synchrotron X-ray fluorescence microscopy

The osteochondral interface is a thin layer that connects hyaline cartilage to subchondral bone. Subcellular elemental distribution can be visualised using synchrotron X-ray fluorescence microscopy (SR-XFM) (1 μm). This study aims to determine the relationship between elemental distribution and osteoarthritis (OA) progression based on disease severity. Using modified Mankin scores, we collected tibia plates from 9 knee OA patients who underwent knee replacement surgery and graded them as intact cartilage (non-OA) or degraded cartilage (OA). We used a tape-assisted system with a silicon nitride sandwich structure to collect fresh-frozen osteochondral sections, and changes in the osteochondral unit were defined using quantified SR-XFM elemental mapping at the Australian synchrotron's XFM beamline. Non-OA osteochondral samples were found to have significantly different zinc (Zn) and calcium (Ca) compositions than OA samples. The tidemark separating noncalcified and calcified cartilage was rich in zinc. Zn levels in OA samples were lower than in non-OA samples (P = 0.0072). In OA samples, the tidemark had less Ca than the calcified cartilage zone and subchondral bone plate (P < 0.0001). The Zn-strontium (Sr) colocalisation index was higher in OA samples than in non-OA samples. The lead, potassium, phosphate, sulphur, and chloride distributions were not significantly different (P > 0.05). In conclusion, SR-XFM analysis revealed spatial elemental distribution at the subcellular level during OA development.

Physiological responses of plants to in vivo X-ray damage from X-ray fluorescence measurements: insights from anatomical, elemental, histochemical, and ultrastructural analyses

X-ray fluorescence spectroscopy (XRF) is a powerful technique for the in vivo assessment of plant tissues. However, the potential X-ray exposure damages might affect the structure and elemental composition of living plant tissues leading to artefacts in the recorded data. Herein, we exposed in vivo soybean (Glycine max (L.) Merrill) leaves to several X-ray doses through a polychromatic benchtop microprobe X-ray fluorescence spectrometer, modulating the photon flux density by adjusting either the beam size, current or exposure time. Changes in the irradiated plant tissues' structure, ultrastructure and physiology were investigated through light and transmission electron microscopy (TEM). Depending X-ray exposure dose, decreased K and X-ray scattering intensities and increased Ca, P, and Mn signals on soybean leaves were recorded. Anatomical analysis indicated the necrosis of epidermal and mesophyll cells on the irradiated spots, where TEM images revealed the collapse of cytoplasm and cell wall breaking. Furthermore, the histochemical analysis detected the production of reactive oxygen species and the inhibition of chlorophyll autofluorescence in these areas. Under certain X-ray exposure conditions, e.g., high photon flux density and long exposure time, XRF measurements may affect the soybean leaves structures, elemental composition, and cellular ultrastructure, and induce programmed cell death (PCD). Our characterisation shed light on the plant's responses to the X-ray-induced radiation damage and might help to establish proper X-ray radiation limits and novel strategies for in vivo benchtop-XRF analysis of vegetal materials.

Microbially influenced tungsten mobilization and formation of secondary minerals in wolframite tailings

Wolframite [(Fe,Mn)WO₄] tailings represent a hazardous waste that can pose a threat to the environment, humans, animals and plants. The present study aims to conduct a high-resolution depth profile characterization of wolframite tailings from Wolfram Camp, North Queensland, Australia, to understand the biogeochemical influences on W mobilization. Several indigenous Fe- and S-oxidizing bacteria (e.g., Streptococcus pneumoniae and Thiomonas delicata) in wolframite tailings were found highly associated with W, As, and rare earth elements. Biooxidation of metal sulfides, i.e., pyrite, molybdenite and bismuthinite, produced sulfuric acid, which accelerated the weathering of wolframite, mobilizing tungstate (WO₄^2-). Using synchrotron-based X-ray fluorescence microscopy (XFM) and W L-edge X-ray absorption near-edge spectroscopy (µ-XANES) analysis, wolframite was initially transformed into Na- and Bi- tungstate as well as tungstic acid (partial weathering) followed by the formation of Ga- and Zn- tungstate after extensive weathering, i.e., the wolframite had disappeared. While W (VI) was the major W species in wolframite tailings, minor W(0) and W(II), and trace W(IV) were also detected. The major contaminant in the Wolfram Camp tailings was As. Though wolframite tailings are hazardous waste, the toxicity of W was unclear. Tungsten waste still has industrial value; apart from using them as substitution material for cement and glass production, there is interest in reprocessing W waste for valuable metal recovery. If the environmental benefits are taken into consideration, i.e., preventing the release of toxic metals into surrounding waterways, reprocessing may be economic.

Alteration history of Séítah formation rocks inferred by PIXL x-ray fluorescence, x-ray diffraction, and multispectral imaging on Mars

Collocated crystal sizes and mineral identities are critical for interpreting textural relationships in rocks and testing geological hypotheses, but it has been previously impossible to unambiguously constrain these properties using in situ instruments on Mars rovers. Here, we demonstrate that diffracted and fluoresced x-rays detected by the PIXL instrument (an x-ray fluorescence microscope on the Perseverance rover) provide information about the presence or absence of coherent crystalline domains in various minerals. X-ray analysis and multispectral imaging of rocks from the Séítah formation on the floor of Jezero crater shows that they were emplaced as coarsely crystalline igneous phases. Olivine grains were then partially dissolved and filled by finely crystalline or amorphous secondary silicate, carbonate, sulfate, and chloride/oxychlorine minerals. These results support the hypothesis that Séítah formation rocks represent olivine cumulates altered by fluids far from chemical equilibrium at low water-rock ratios.

An olivine cumulate outcrop on the floor of Jezero crater, Mars

The geological units on the floor of Jezero crater, Mars, are part of a wider regional stratigraphy of olivine-rich rocks, which extends well beyond the crater. We investigate the petrology of olivine and carbonate-bearing rocks of the Séítah formation in the floor of Jezero. Using multispectral images and x-ray fluorescence data, acquired by the Perseverance rover, we performed a petrographic analysis of the Bastide and Brac outcrops within this unit. We find that these outcrops are composed of igneous rock, moderately altered by aqueous fluid. The igneous rocks are mainly made of coarse-grained olivine, similar to some Martian meteorites. We interpret them as an olivine cumulate, formed by settling and enrichment of olivine through multi-stage cooling of a thick magma body.

High-speed free-run ptychography at the Australian Synchrotron

Over the last decade ptychography has progressed rapidly from a specialist ultramicroscopy technique into a mature method accessible to non-expert users. However, to improve scientific value ptychography data must reconstruct reliably, with high image quality and at no cost to other correlative methods. Presented here is the implementation of high-speed ptychography used at the Australian Synchrotron on the XFM beamline, which includes a free-run data collection mode where dead time is eliminated and the scan time is optimized. It is shown that free-run data collection is viable for fast and high-quality ptychography by demonstrating extremely high data rate acquisition covering areas up to 352 000 µm² at up to 140 µm² s^-1, with 13× spatial resolution enhancement compared with the beam size. With these improvements, ptychography at velocities up to 250 µm s^-1 is approaching speeds compatible with fast-scanning X-ray fluorescence microscopy. The combination of these methods provides morphological context for elemental and chemical information, enabling unique scientific outcomes.

An integrated mass spectrometry imaging and digital pathology workflow for objective detection of colorectal tumours by unique atomic signatures

Tumours are abnormal growths of cells that reproduce by redirecting essential nutrients and resources from surrounding tissue. Changes to cell metabolism that trigger the growth of tumours are reflected in subtle differences between the chemical composition of healthy and malignant cells. We used LA-ICP-MS imaging to investigate whether these chemical differences can be used to spatially identify tumours and support detection of primary colorectal tumours in anatomical pathology. First, we generated quantitative LA-ICP-MS images of three colorectal surgical resections with case-matched normal intestinal wall tissue and used this data in a Monte Carlo optimisation experiment to develop an algorithm that can classify pixels as tumour positive or negative. Blinded testing and interrogation of LA-ICP-MS images with micrographs of haematoxylin and eosin stained and Ki67 immunolabelled sections revealed Monte Carlo optimisation accurately identified primary tumour cells, as well as returning false positive pixels in areas of high cell proliferation. We analysed an additional 11 surgical resections of primary colorectal tumours and re-developed our image processing method to include a random forest regression machine learning model to correctly identify heterogenous tumours and exclude false positive pixels in images of non-malignant tissue. Our final model used over 1.6 billion calculations to correctly discern healthy cells from various types and stages of invasive colorectal tumours. The imaging mass spectrometry and data analysis methods described, developed in partnership with clinical cancer researchers, have the potential to further support cancer detection as part of a comprehensive digital pathology approach to cancer care through validation of a new chemical biomarker of tumour cells.

Simultaneous structural and elemental nano-imaging of human brain tissue

Examining chemical and structural characteristics of micro-features in complex tissue matrices is essential for understanding biological systems. Advances in multimodal chemical and structural imaging using synchrotron radiation have overcome many issues in correlative imaging, enabling the characterization of distinct microfeatures at nanoscale resolution in ex vivo tissues. We present a nanoscale imaging method that pairs X-ray ptychography and X-ray fluorescence microscopy (XFM) to simultaneously examine structural features and quantify elemental content of microfeatures in complex ex vivo tissues. We examined the neuropathological microfeatures Lewy bodies, aggregations of superoxide dismutase 1 (SOD1) and neuromelanin in human post-mortem Parkinson's disease tissue. Although biometals play essential roles in normal neuronal biochemistry, their dyshomeostasis is implicated in Parkinson's disease aetiology. Here we show that Lewy bodies and SOD1 aggregates have distinct elemental fingerprints yet are similar in structure, whilst neuromelanin exhibits different elemental composition and a distinct, disordered structure. The unique approach we describe is applicable to the structural and chemical characterization of a wide range of complex biological tissues at previously unprecedented levels of detail.

Structural and chemical characterisation of microfeatures in unadulterated Parkinson's disease brain tissue using synchrotron nanoscale XFM and ptychography.

Iterative energy self-calibration of Fe XANES spectra. Erratum

A correction is made to the paper by Jones et al. (2020). [J. Synchrotron Rad. (2020), 27, 207-211].

Concentrations of toxic metals and essential trace elements vary among individual neurons in the human locus ceruleus

Objective

Damage to locus ceruleus neurons could play a part in the pathogenesis of neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, and multiple sclerosis because of impairment of the blood-brain barrier and enhanced neuroinflammation. The locus ceruleus has connections throughout the brain and spinal cord, so the characteristic widespread multifocal pathology in these disorders could be due to damage to different subsets of locus ceruleus neurons. Previous studies have shown that only certain locus ceruleus neurons accumulate the neurotoxic metal mercury. To find out if concentrations of other toxic metals or of essential trace elements also vary between individual locus ceruleus neurons, we used synchrotron X-ray fluorescence microscopy on frozen sections of locus ceruleus neurons taken from people with multiple sclerosis, in whom the locus ceruleus is structurally intact.

Materials and methods

Paraffin embedded sections containing the locus ceruleus from seven people with multiple sclerosis were stained with autometallography that demonstrates accumulations of mercury, silver and bismuth. These were compared to maps of multiple elements obtained from frozen sections of locus ceruleus neurons from the same people using X-ray fluorescence microscopy. Neurons in the anterior pons from three of these donors were used as internal controls.

Results

Autometallography staining was observed in scattered locus ceruleus neurons from three of the seven donors. X-ray fluorescence microscopy showed variations among individual locus ceruleus neurons in levels of mercury, selenium, iron, copper, lead, bromine, and rubidium. Variations between donors of locus ceruleus neuronal average levels of mercury, iron, copper, and bromine were also detected. Anterior pons neurons contained no mercury, had varied levels of iron, and had lower copper levels than locus ceruleus neurons.

Conclusions

Individual human locus ceruleus neurons contain varying levels of toxic metals and essential trace elements. In contrast, most toxic metals are absent or at low levels in nearby anterior pons neurons. The locus ceruleus plays a role in numerous central nervous system functions, including maintaining the blood-brain-barrier and limiting neuroinflammation. Toxic metals, or alterations in essential trace metals within individual locus ceruleus neurons, could be one factor determining the non-random destruction of locus ceruleus neurons in normal aging and neurodegenerative diseases, and subsequently the sites of the widespread multifocal central nervous system pathology in these disorders.

Elemental characterisation of the pyramidal neuron layer within the rat and mouse hippocampus

A unique combination of sensitivity, resolution, and penetration make X-ray fluorescence imaging (XFI) ideally suited to investigate trace elemental distributions in the biological context. XFI has gained widespread use as an analytical technique in the biological sciences, and in particular enables exciting new avenues of research in the field of neuroscience. In this study, elemental mapping by XFI was applied to characterise the elemental content within neuronal cell layers of hippocampal sub-regions of mice and rats. Although classical histochemical methods for metal detection exist, such approaches are typically limited to qualitative analysis. Specifically, histochemical methods are not uniformly sensitive to all chemical forms of a metal, often displaying variable sensitivity to specific "pools" or chemical forms of a metal. In addition, histochemical methods require fixation and extensive chemical treatment of samples, creating the strong likelihood for metal redistribution, leaching, or contamination. Direct quantitative elemental mapping of total elemental pools, in situ within ex vivo tissue sections, without the need for chemical fixation or addition of staining reagents is not possible with traditional histochemical methods; however, such a capability, which is provided by XFI, can offer an enormous analytical advantage. The results we report herein demonstrate the analytical advantage of XFI elemental mapping for direct, label-free metal quantification, in situ within ex vivo brain tissue sections. Specifically, we definitively characterise for the first time, the abundance of Fe within the pyramidal cell layers of the hippocampus. Localisation of Fe to this cell layer is not reproducibly achieved with classical Perls histochemical Fe stains. The ability of XFI to directly quantify neuronal elemental (P, S, Cl, K, Ca, Fe, Cu, Zn) distributions, revealed unique profiles of Fe and Zn within anatomical sub-regions of the hippocampus i.e., cornu ammonis 1, 2 or 3 (CA1, CA2 or CA3) sub-regions. Interestingly, our study reveals a unique Fe gradient across neuron populations within the non-degenerating and pathology free rat hippocampus, which curiously mirrors the pattern of region-specific vulnerability of the hippocampus that has previously been established to occur in various neurodegenerative diseases.

Assessing radiation dose limits for X-ray fluorescence microscopy analysis of plant specimens

BACKGROUND AND AIMS

X-ray fluorescence microscopy (XFM) is a powerful technique to elucidate the distribution of elements within plants. However, accumulated radiation exposure during analysis can lead to structural damage and experimental artefacts including elemental redistribution. To date, acceptable dose limits have not been systematically established for hydrated plant specimens.

METHODS

Here we systematically explore acceptable dose rate limits for investigating fresh sunflower (Helianthus annuus) leaf and root samples and investigate the time-dose damage in leaves attached to live plants.

KEY RESULTS

We find that dose limits in fresh roots and leaves are comparatively low (4.1 kGy), based on localized disintegration of structures and element-specific redistribution. In contrast, frozen-hydrated samples did not incur any apparent damage even at doses as high as 587 kGy. Furthermore, we find that for living plants subjected to XFM measurement in vivo and grown for a further 9 d before being reimaged with XFM, the leaves display elemental redistribution at doses as low as 0.9 kGy and they continue to develop bleaching and necrosis in the days after exposure.

CONCLUSIONS

The suggested radiation dose limits for studies using XFM to examine plants are important for the increasing number of plant scientists undertaking multidimensional measurements such as tomography and repeated imaging using XFM.

Iterative energy self-calibration of Fe XANES spectra

Determining the oxidation state of Fe through parameterization of X-ray absorption near-edge structure (XANES) spectral features is highly dependent on accurate and repeatable energy calibration between spectra. Small errors in energy calibration can lead to vastly different interpretations. While simultaneous measurement of a reference foil is often undertaken on X-ray spectroscopy beamlines, other beamlines measure XANES spectra without a reference foil and therefore lack a method for correcting energy drift. Here a method is proposed that combines two measures of Fe oxidation state taken from different parts of the spectrum to iteratively correct for an unknown energy offset between spectra, showing successful iterative self-calibration not only during individual beam time but also across different beamlines.

Monitoring compositional changes in Ni(OH)2 electrocatalysts employed in the oxygen evolution reaction

Relating morphology and compositional changes spatially across a catalyst is important for understanding the active site involved in a reaction which is studied here for the OER at Ni(OH)₂.

Simultaneous nanostructure and chemical imaging of intact whole nematodes

Accurately locating biologically relevant elements at high resolution: simultaneous ptychography and fluorescence imaging of large specimens comes of age.

X-ray fluorescence microscopic measurement of elemental distribution in the mouse retina with age

The biologically important metals such as zinc, copper and iron play key roles in retinal function, yet no study has mapped the spatio-temporal distribution of retinal biometals in healthy or diseased retina. We investigated a natural mouse model of retinal degeneration, the Cln6^nclf mouse. As dysfunctional metabolism of biometals is observed in the brains of these animals and deregulated metal homeostasis has been linked to retinal degeneration, we focused on mapping the elemental distribution in the healthy and Cln6^nclf mouse retina with age. Retinal and RPE elemental homeostasis was mapped in Cln6^nclf and C57BL6/J mice from 1 to 8 months of age using X-ray Fluorescence Microscopy at the Australian Synchrotron. In the healthy retina, we detected a progressive loss of phosphorus in the outer nuclear layer and significant reduction in iron in the inner segments of the photoreceptors. Further investigation revealed a unique elemental signature for each retinal layer, with high areal concentrations of iron and sulfur in the photoreceptor segments and calcium, phosphorus, zinc and potassium enrichment predominantly in the nuclear layers. The analysis of retinae from Cln6^nclf mice did not show significant temporal changes in elemental distributions compared to age matched controls, despite significant photoreceptor cell loss. Our data therefore demonstrates that retinal layers have unique elemental composition. Elemental distribution is, with few exceptions, stably maintained over time in healthy and Cln6^nclf mouse retina, suggesting conservation of elemental distribution is critical for basic retinal function with age and is not modulated by processes underlying retinal degeneration.

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered 'random'. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C₆₀. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C₆₀ were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.

High-resolution complementary chemical imaging of bio-elements in Caenorhabditis elegans

Here, we present a sub-μm multimodal approach to image essential elements in Caenorhabditis elegans. A combination of chemical imaging technologies reveals total metal concentration, chemical state and the protein to which an element is associated. This application of distinct yet complementary chemical imaging techniques provided unique insight into essential and trace elements at the subcellular level.

X-ray laser-induced electron dynamics observed by femtosecond diffraction from nanocrystals of Buckminsterfullerene

X-ray free-electron lasers (XFELs) deliver x-ray pulses with a coherent flux that is approximately eight orders of magnitude greater than that available from a modern third-generation synchrotron source. The power density of an XFEL pulse may be so high that it can modify the electronic properties of a sample on a femtosecond time scale. Exploration of the interaction of intense coherent x-ray pulses and matter is both of intrinsic scientific interest and of critical importance to the interpretation of experiments that probe the structures of materials using high-brightness femtosecond XFEL pulses. We report observations of the diffraction of extremely intense 32-fs nanofocused x-ray pulses by a powder sample of crystalline C60. We find that the diffraction pattern at the highest available incident power significantly differs from the one obtained using either third-generation synchrotron sources or XFEL sources operating at low output power and does not correspond to the diffraction pattern expected from any known phase of crystalline C60. We interpret these data as evidence of a long-range, coherent dynamic electronic distortion that is driven by the interaction of the periodic array of C60 molecular targets with intense x-ray pulses of femtosecond duration.

Simultaneous X-ray fluorescence and scanning X-ray diffraction microscopy at the Australian Synchrotron XFM beamline

Owing to its extreme sensitivity, quantitative mapping of elemental distributions via X-ray fluorescence microscopy (XFM) has become a key microanalytical technique. The recent realisation of scanning X-ray diffraction microscopy (SXDM) meanwhile provides an avenue for quantitative super-resolved ultra-structural visualization. The similarity of their experimental geometries indicates excellent prospects for simultaneous acquisition. Here, in both step- and fly-scanning modes, robust, simultaneous XFM-SXDM is demonstrated.

Molar concentration from sequential 2-D water-window X-ray ptychography and X-ray fluorescence in hydrated cells

Recent developments in biological X-ray microscopy have allowed structural information and elemental distribution to be simultaneously obtained by combining X-ray ptychography and X-ray fluorescence microscopy. Experimentally, these methods can be performed simultaneously; however, the optimal conditions for each measurement may not be compatible. Here, we combine two distinct measurements of ultrastructure and elemental distribution, with each measurement performed under optimised conditions. By combining optimised ptychography and fluorescence information we are able to determine molar concentrations from two-dimensional images, allowing an investigation into the interactions between the environment sensing filopodia in fibroblasts and extracellular calcium. Furthermore, the biological ptychography results we present illustrate a point of maturity where the technique can be applied to solve significant problems in structural biology.

Elemental mapping of the entire intact Drosophila gastrointestinal tract

The main role of the animal gastrointestinal (GI) tract is the selective absorption of dietary nutrients from ingested food sources. One class of vital micronutrients are the essential biometals such as copper, zinc and iron, which participate in a plethora of biological process, acting as enzymatic or structural co-factors for numerous proteins and also as important cellular signalling molecules. To help elucidate the mechanisms by which biometals are absorbed from the diet, we mapped elemental distribution in entire, intact Drosophila larval GI tracts using synchrotron X-ray fluorescence microscopy. Our results revealed distinct regions of the GI tract enriched for specific metals. Copper was found to be concentrated in the copper cell region but also in the region directly anterior to the copper cells and unexpectedly, in the middle midgut/iron cell region as well. Iron was observed exclusively in the iron cell region, confirming previous work with iron-specific histological stains. Zinc was observed throughout the GI tract with an increased accumulation in the posterior midgut region, while manganese was seen to co-localize with calcium specifically in clusters in the distal Malpighian tubules. This work simultaneously reveals distribution of a number of biologically important elements in entire, intact GI tracts. These distributions revealed not only a previously undescribed Ca/Mn co-localization, but also the unexpected presence of additional Cu accumulations in the iron cell region.

Mapping biological composition through quantitative phase and absorption X-ray ptychography

Isolating compositional information in biological X-ray imaging can be problematic as such information is conflated with thickness and density variations when viewing in projection through a sample. We demonstrate an effective method for identifying variations in material composition by simultaneously using the quantitative phase and magnitude images provided through soft X-ray ptychography. Using this approach we show significantly increased contrast and improved reliability of the identification of intracellular features from uncharacterised samples. While demonstrated for X-ray ptychography, this method is immediately applicable to electron and optical microscopy methods where the complex transmission function of the sample is recovered.

Whole-cell phase contrast imaging at the nanoscale using Fresnel coherent diffractive imaging tomography

X-ray tomography can provide structural information of whole cells in close to their native state. Radiation-induced damage, however, imposes a practical limit to image resolution, and as such, a choice between damage, image contrast, and image resolution must be made. New coherent diffractive imaging techniques, such Fresnel Coherent Diffractive Imaging (FCDI), allows quantitative phase information with exceptional dose efficiency, high contrast, and nano-scale resolution. Here we present three-dimensional quantitative images of a whole eukaryotic cell by FCDI at a spatial resolution below 70 nm with sufficient phase contrast to distinguish major cellular components. From our data, we estimate that the minimum dose required for a similar resolution is close to that predicted by the Rose criterion, considerably below accepted estimates of the maximum dose a frozen-hydrated cell can tolerate. Based on the dose efficiency, contrast, and resolution achieved, we expect this technique will find immediate applications in tomographic cellular characterisation.

Phase-diverse Fresnel coherent diffractive imaging of malaria parasite-infected red blood cells in the water window

Phase-diverse Fresnel coherent diffractive imaging has been shown to reveal the structure and composition of biological specimens with high sensitivity at nanoscale resolution. However, the method has yet to be applied using X-ray illumination with energy in the so-called 'water-window' that lies between the carbon and oxygen K edges. In this range, differences in the strength of the X-ray interaction for protein based biological materials and water is increased. Here we demonstrate a proof-of-principle application of FCDI at an X-ray energy within the water-window to a dehydrated cellular sample composed of red blood cells infected with the trophozoite stage of the malaria parasite, Plasmodium falciparum. Comparison of the results to both optical and electron microscopy shows that the correlative imaging methods that include water-window FCDI will find utility in studying cellular architecture.

Application of a complex constraint for biological samples in coherent diffractive imaging

We demonstrate the application of a complex constraint in the reconstruction of images from phase-diverse Fresnel coherent diffraction data for heterogeneous biological objects. The application of this constraint is shown to improve the quality of the reconstruction of both the phase and the magnitude of the complex object transmission function.