Biological applications of X-ray fluorescence microscopy: exploring the subcellular topography and speciation of transition metals

Simple in vitro method to evaluate ZIP zinc transport ability through zinc transporter 1 and metallothionein expression measurements

Measuring the cellular zinc content and examining the alteration of zinc status are critical for investigating the cellular homeostasis and dynamics of zinc and its involvement in patho-physiological functions. Many Zrt- and Irt-related protein (ZIP) transporters uptake zinc from the extracellular space. Among Zn transporters (ZNTs), ZNT1 effluxes cytosolic zinc. As cytosolic zinc-binding proteins, metallothioneins (MTs) also contribute to the control of cellular zinc homeostasis. Systemic and cellular zinc homeostasis is considered to be maintained by balancing expression and functional activities of these proteins. The zinc transport ability of ZIPs is typically measured by evaluating cellular zinc content with various zinc-detection methods and systems. Many small-molecule fluorescent probes and fluorescence resonance energy transfer-based protein sensors have been exploited for this purpose. Although powerful analytical methods using special instruments have been developed to quantify zinc, they are often not easily accessible. Here, we present a simplified and inexpensive method to estimate the zinc transport ability of ZIP transporters using the expression responses of ZNT1 and MT. This protocol should be effective in several applications because ZNT1 and MT expression are easily evaluated by immunoblotting and immunofluorescence staining as basic biochemical techniques available in most laboratories. This method is advantageous for examining the relative zinc status or alterations mediated by expression changes of ZIPs in cells cultured in normal medium without zinc supplementation. As zinc is an essential micronutrient, extensive research is necessary to improve dietary zinc absorption to promote health. Therefore, we also propose a simple screening method of foods to improve zinc absorption as an application of measuring ZIP-mediated MT expression.

The development and use of metal-based probes for X-ray fluorescence microscopy

X-ray fluorescence microscopy (XFM) has become a widely used technique for imaging the concentration and distribution of metal ions in cells and tissues. Recent advances in synchrotron sources, optics, and detectors have improved the spatial resolution of the technique to <10 nm with attogram detection sensitivity. However, to make XFM most beneficial for bioimaging-especially at the nanoscale-the metal ion distribution must be visualized within the subcellular context of the cell. Over the years, a number of approaches have been taken to develop X-ray-sensitive tags that permit the visualization of specific organelles or proteins using XFM. In this review, we examine the types of X-ray fluorophore used, including nanomaterials and metal ions, and the approaches used to incorporate the metal into their target binding site via antibodies, genetically encoded metal-binding peptides, affinity labeling, or cell-specific peptides. We evaluate their advantages and disadvantages, review the scientific findings, and discuss the needs for future development.

In-situ x-ray fluorescence imaging of the endogenous iodine distribution in murine thyroids

X-ray fluorescence imaging (XFI) is a non-invasive detection method of small quantities of elements, which can be excited to emit fluorescence x-ray photons upon irradiation with an incident x-ray beam. In particular, it can be used to measure nanoparticle uptake in cells and tissue, thus making it a versatile medical imaging modality. However, due to substantially increased multiple Compton scattering background in the measured x-ray spectra, its sensitivity severely decreases for thicker objects, so far limiting its applicability for tracking very small quantities under in-vivo conditions. Reducing the detection limit would enable the ability to track labeled cells, promising new insights into immune response and pharmacokinetics. We present a synchrotron-based approach for reducing the minimal detectable marker concentration by demonstrating the feasibility of XFI for measuring the yet inaccessible distribution of the endogenous iodine in murine thyroids under in-vivo conform conditions. This result can be used as a reference case for the design of future preclinical XFI applications as mentioned above.

Recent advances in copper analyses by inorganic mass spectrometry

Copper (Cu) participates in the biological redox reaction in the body, and its deficiency is fatal to the body. At the same time, Cu is extremely toxic when it exists in excess. Thus, the body has to tightly and spatiotemporally regulate the concentration of Cu within a physiological range by several groups of Cu-regulating proteins. However, entire mechanisms underlying the maintenance of Cu homeostasis in body and cells have not fully understood. It is necessary to analyze Cu itself in a body and in a cell to reveal the Cu homeostasis. In this review, recent advances in the analytical techniques to understand the Cu metabolism such as speciation, imaging and single-cell analysis of Cu were highlighted.

MOLGENGO: Finding Novel Molecules with Desired Electronic Properties by Capitalizing on Their Global Optimization

The discovery of novel and favorable fluorophores is critical for understanding many chemical and biological studies. High-resolution biological imaging necessitates fluorophores with diverse colors and high quantum yields. The maximum oscillator strength and its corresponding absorption wavelength of a molecule are closely related to the quantum yields and the emission spectrum of fluorophores, respectively. Thus, the core step to design favorable fluorophore molecules is to optimize the desired electronic transition properties of molecules. Here, we present MOLGENGO, a new molecular property optimization algorithm, to discover novel and favorable fluorophores with machine learning and global optimization. This study reports novel molecules from MOLGENGO with high oscillator strength and absorption wavelength close to 200, 400, and 600 nm. The results of MOLGENGO simulations have the potential to be candidates for new fluorophore frameworks.

Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants

Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.

X-ray fluorescence microscopy scanning of Drosophila oocytes and eggs

X-ray fluorescence microscopy (XFM) is a powerful tool for mapping and quantifying the spatial distribution of elemental composition of biological samples. Recently, it was reported that transition metal fluctuations occur during Drosophila reproduction, analogous to what is seen in mammals and nematodes, and may contribute to Drosophila female fertility. To further support XFM studies on Drosophila reproduction, we describe procedures for isolating oocytes and activated eggs and examining their elemental composition by XFM scanning and analysis. For complete details on the use and execution of this protocol, please refer to Hu et al. (2020).

Imaging inorganic nanomaterial fate down to the organelle level

Nanotoxicology remains an important and emerging field since only recent years have seen the improvement of biological models and exposure setups toward real-life scenarios. The appropriate analysis of nanomaterial fate in these conditions also required methodological developments in imaging to become sensitive enough and element specific. In the last 2-4 years, impressive breakthroughs have been achieved using electron microscopy, nanoscale secondary ion mass spectrometry, X-ray fluorescence microscopy, or fluorescent sensors. In this review, basics of the approaches and application examples in the study of nanomaterial fate in biological systems will be described to highlight recent successes in the field.

Simultaneous Zn2+ tracking in multiple organelles using super-resolution morphology-correlated organelle identification in living cells

Zn²⁺ plays important roles in metabolism and signaling regulation. Subcellular Zn²⁺ compartmentalization is essential for organelle functions and cell biology, but there is currently no method to determine Zn²⁺ signaling relationships among more than two different organelles with one probe. Here, we report simultaneous Zn²⁺ tracking in multiple organelles (Zn-STIMO), a method that uses structured illumination microscopy (SIM) and a single Zn²⁺ fluorescent probe, allowing super-resolution morphology-correlated organelle identification in living cells. To guarantee SIM imaging quality for organelle identification, we develop a new turn-on Zn²⁺ fluorescent probe, NapBu-BPEA, by regulating the lipophilicity of naphthalimide-derived Zn²⁺ probes to make it accumulate in multiple organelles except the nucleus. Zn-STIMO with this probe shows that CCCP-induced mitophagy in HeLa cells is associated with labile Zn²⁺ enhancement. Therefore, direct organelle identification supported by SIM imaging makes Zn-STIMO a reliable method to determine labile Zn²⁺ dynamics in various organelles with one probe. Finally, SIM imaging of pluripotent stem cell-derived organoids with NapBu-BPEA demonstrates the potential of super-resolution morphology-correlated organelle identification to track biospecies and events in specific organelles within organoids.

Subcellular Zn²⁺ compartmentalisation is essential for cell biology. Here the authors make a turn-on fluorescent Zn²⁺ probe that localises to multiple organelles, and correlate its location using organelle morphology derived from structured illumination microscopy.

Development of a multi-detector readout circuitry for ultrahigh energy resolution single-photon imaging applications

In this paper, we present the design and preliminary performance evaluation of a novel external multi-channel readout circuitry for small-pixel room-temperature semiconductor detectors, namely CdZnTe (CZT) and CdTe, that provide an excellent intrinsic spatial (250 and 500 μm pixel size) and an ultrahigh energy resolution (~1% at 122 keV) for X-ray and gamma-ray imaging applications. An analog front-end printed circuit board (PCB) was designed and developed for data digitization, data transfer and ASIC control of pixelated CZT or CdTe detectors. Each detector unit is 2 cm × 2 cm in size and 1 or 2 mm in thickness, being bump-bonded onto a HEXITEC ASIC, and wire-bonded to a readout detector module PCB. The detectors' front-end is then connected, through flexible cables of up to 10 m in length, to a remote data acquisition system that interfaces with a PC through USB3.0 connection. We present the design and performance of a prototype multi-channel readout system that can read out up to 24 detector modules synchronously. Our experimental results demonstrated that the readout circuitry offers an ultrahigh spectral resolution (0.8 keV at 60 keV and 1.05 keV at 122 keV) with the Cd(Zn)Te/HEXITEC ASIC modules tested. This architecture was designed to allow easy expansion to accommodate a larger number of detector modules, and the flexibility of arranging the detector modules in a large and deformable detector array without degrading the excellent energy resolution.

Impact of Neospora caninum Infection on the Bioenergetics and Transcriptome of Cerebrovascular Endothelial Cells

In this work, the effects of the protozoan Neospora caninum on the bioenergetics, chemical composition, and elemental content of human brain microvascular endothelial cells (hBMECs) were investigated. We showed that N. caninum can impair cell mitochondrial (Mt) function and causes an arrest in host cell cycling at S and G2 phases. These adverse effects were also associated with altered expression of genes involved in Mt energy metabolism, suggesting Mt dysfunction caused by N. caninum infection. Fourier Transform Infrared (FTIR) spectroscopy analysis of hBMECs revealed alterations in the FTIR bands as a function of infection, where infected cells showed alterations in the absorption bands of lipid (2924 cm⁻¹), amide I protein (1649 cm⁻¹), amide II protein (1537 cm⁻¹), nucleic acids and carbohydrates (1092 cm⁻¹, 1047 cm⁻¹, and 939 cm⁻¹). By using quantitative synchrotron radiation X-ray fluorescence (μSR-XRF) imaging and quantification of the trace elements Zn, Cu and Fe, we detected an increase in the levels of Zn and Cu from 3 to 24 h post infection (hpi) in infected cells compared to control cells, but there were no changes in the level of Fe. We also used Affymetrix array technology to investigate the global alteration in gene expression of hBMECs and rat brain microvascular endothelial cells (rBMVECs) in response to N. caninum infection at 24 hpi. The result of transcriptome profiling identified differentially expressed genes involved mainly in immune response, lipid metabolism and apoptosis. These data further our understanding of the molecular events that shape the interaction between N. caninum and blood-brain-barrier endothelial cells.

Nano-imaging trace elements at organelle levels in substantia nigra overexpressing α-synuclein to model Parkinson's disease

Sub-cellular trace element quantifications of nano-heterogeneities in brain tissues offer unprecedented ways to explore at elemental level the interplay between cellular compartments in neurodegenerative pathologies. We designed a quasi-correlative method for analytical nanoimaging of the substantia nigra, based on transmission electron microscopy and synchrotron X-ray fluorescence. It combines ultrastructural identifications of cellular compartments and trace element nanoimaging near detection limits, for increased signal-to-noise ratios. Elemental composition of different organelles is compared to cytoplasmic and nuclear compartments in dopaminergic neurons of rat substantia nigra. They exhibit 150–460 ppm of Fe, with P/Zn/Fe-rich nucleoli in a P/S-depleted nuclear matrix and Ca-rich rough endoplasmic reticula. Cytoplasm analysis displays sub-micron Fe/S-rich granules, including lipofuscin. Following AAV-mediated overexpression of α-synuclein protein associated with Parkinson’s disease, these granules shift towards higher Fe concentrations. This effect advocates for metal (Fe) dyshomeostasis in discrete cytoplasmic regions, illustrating the use of this method to explore neuronal dysfunction in brain diseases.

Lemelle et al. describe the use of TEM and synchrotron X-ray fluorescence for quasi-correlative nanoimaging and sub-cellular trace element quantification of rat brain tissue. They further observe elemental (iron and sulfur) dyshomeostasis in cytoplasmic granules when overexpressing α-synuclein protein associated with Parkinson’s disease, demonstrating the usefulness of this method to further explore dysfunctions at organelle levels in brain diseases.

Elemental quantification and analysis of structural abnormalities in neurons from Parkinson's-diseased brains by X-ray fluorescence microscopy and diffraction

In this work we use scanning X-ray microscopy to study the structure and elemental composition of neuromelanin-positive neurons in substantia nigra tissue of Parkinson patients (PD) and controls. A total of 53 neurons were analyzed with X-ray fluorescence (XRF) and diffraction using sub-µm-focused synchrotron radiation. A statistical evaluation identified copper as the most group-discriminating element and indicated that interindividual and intraindividual variations are of great relevance in tissue measurements of diseased patients and prevent from automated group clustering. XRF analyses of two Lewy bodies (LBs) highlight a heterogeneity in elemental distributions in these LBs, whereas an innovative X-ray diffraction-based method approach was used to reveal β-sheet-rich crystalline structures in LBs. Overall, sub-µm-focus X-ray microscopy highlighted the elemental heterogeneity in PD pathology.

2D MEMS-based multilayer Laue lens nanofocusing optics for high-resolution hard x-ray microscopy

We report on the development of 2D integrated multilayer Laue lens (MLL) nanofocusing optics used for high-resolution x-ray microscopy. A Micro-Electro-Mechanical-Systems (MEMS) - based template has been designed and fabricated to accommodate two linear MLL optics in pre-aligned configuration. The orthogonality requirement between two MLLs has been satisfied to a better than 6 millidegrees level, and the separation along the x-ray beam direction was controlled on a micrometer scale. Developed planar 2D MLL structure has demonstrated astigmatism free point focus of ∼14 nm by ∼13 nm in horizontal and vertical directions, respectively, at 13.6 keV photon energy. Approaching 10 nm resolution with integrated 2D MLL optic is a significant step forward in applications of multilayer Laue lenses for high-resolution hard x-ray microscopy and their adoption by the general x-ray microscopy community.

Intracellular location matters: rationalization of the anti-inflammatory activity of a manganese(ii) superoxide dismutase mimic complex

The study of Mn-based superoxide dismutase mimic conjugated with a multimodal Re-probe in a cellular model of oxidative stress revealed that its bioactivity is associated with its accumulation at the mitochondria.

Spatially Resolved Dissolution and Speciation Changes of ZnO Nanorods during Short-Term in Situ Incubation in a Simulated Wastewater Environment

Zinc oxide engineered nanomaterials (ZnO ENMs) are used in a variety of applications worldwide due to their optoelectronic and antibacterial properties with potential contaminant risk to the environment following their disposal. One of the main potential pathways for ZnO nanomaterials to reach the environment is via urban wastewater treatment plants. So far there is no technique that can provide spatiotemporal nanoscale information about the rates and mechanisms by which the individual nanoparticles transform. Fundamental knowledge of how the surface chemistry of individual particles change, and the heterogeneity of transformations within the system, will reveal the critical physicochemical properties determining environmental damage and deactivation. We applied a methodology based on spatially resolved in situ X-ray fluorescence microscopy (XFM), allowing observation of real-time dissolution and morphological and chemical evolution of synthetic template-grown ZnO nanorods (∼725 nm length, ∼140 nm diameter). Core-shell ZnO-ZnS nanostructures were formed rapidly within 1 h, and significant amounts of ZnS species were generated, with a corresponding depletion of ZnO after 3 h. Diffuse nanoparticles of ZnS, Zn₃(PO₄)₂, and Zn adsorbed to Fe-oxyhydroxides were also imaged in some nonsterically impeded regions after 3 h. The formation of diffuse nanoparticles was affected by ongoing ZnO dissolution (quantified by inductively coupled plasma mass spectrometry) and the humic acid content in the simulated sludge. Complementary ex situ X-ray absorption spectroscopy and scanning electron microscopy confirmed a significant decrease in the ZnO contribution over time. Application of time-resolved XFM enables predictions about the rates at which ZnO nanomaterials transform during their first stages of the wastewater treatment process.

Metallome of cerebrovascular endothelial cells infected with Toxoplasma gondii using μ-XRF imaging and inductively coupled plasma mass spectrometry

In this study, we measured the levels of elements in human brain microvascular endothelial cells (ECs) infected with T. gondii. ECs were infected with tachyzoites of the RH strain, and at 6, 24, and 48 hours post infection (hpi), the intracellular concentrations of elements were determined using a synchrotron-microfocus X-ray fluorescence microscopy (μ-XRF) system. This method enabled the quantification of the concentrations of Zn and Ca in infected and uninfected (control) ECs at sub-micron spatial resolution. T. gondii-hosting ECs contained less Zn than uninfected cells only at 48 hpi (p < 0.01). The level of Ca was not significantly different between infected and control cells (p > 0.05). Inductively Coupled Plasma Mass Spectrometry (ICP-MS) analysis revealed infection-specific metallome profiles characterized by significant increases in the intracellular levels of Zn, Fe, Mn and Cu at 48 hpi (p < 0.01), and significant reductions in the extracellular concentrations of Co, Cu, Mo, V, and Ag at 24 hpi (p < 0.05) compared with control cells. Zn constituted the largest part (74%) of the total metal composition (metallome) of the parasite. Gene expression analysis showed infection-specific upregulation in the expression of five genes, MT1JP, MT1M, MT1E, MT1F, and MT1X, belonging to the metallothionein gene family. These results point to a possible correlation between T. gondii infection and increased expression of MT1 isoforms and altered intracellular levels of elements, especially Zn and Fe. Taken together, a combined μ-XRF and ICP-MS approach is promising for studies of the role of elements in mediating host-parasite interaction.

Activity-based ratiometric FRET probe reveals oncogene-driven changes in labile copper pools induced by altered glutathione metabolism

Copper is essential for life, and beyond its well-established ability to serve as a tightly bound, redox-active active site cofactor for enzyme function, emerging data suggest that cellular copper also exists in labile pools, defined as loosely bound to low-molecular-weight ligands, which can regulate diverse transition metal signaling processes spanning neural communication and olfaction, lipolysis, rest-activity cycles, and kinase pathways critical for oncogenic signaling. To help decipher this growing biology, we report a first-generation ratiometric fluorescence resonance energy transfer (FRET) copper probe, FCP-1, for activity-based sensing of labile Cu(I) pools in live cells. FCP-1 links fluorescein and rhodamine dyes through a Tris[(2-pyridyl)methyl]amine bridge. Bioinspired Cu(I)-induced oxidative cleavage decreases FRET between fluorescein donor and rhodamine acceptor. FCP-1 responds to Cu(I) with high metal selectivity and oxidation-state specificity and facilitates ratiometric measurements that minimize potential interferences arising from variations in sample thickness, dye concentration, and light intensity. FCP-1 enables imaging of dynamic changes in labile Cu(I) pools in live cells in response to copper supplementation/depletion, differential expression of the copper importer CTR1, and redox stress induced by manipulating intracellular glutathione levels and reduced/oxidized glutathione (GSH/GSSG) ratios. FCP-1 imaging reveals a labile Cu(I) deficiency induced by oncogene-driven cellular transformation that promotes fluctuations in glutathione metabolism, where lower GSH/GSSG ratios decrease labile Cu(I) availability without affecting total copper levels. By connecting copper dysregulation and glutathione stress in cancer, this work provides a valuable starting point to study broader cross-talk between metal and redox pathways in health and disease with activity-based probes.

Analysis of Trace Elements in Human Brain: Its Aim, Methods, and Concentration Levels

Trace elements play a crucial role in many biochemical processes, mainly as components of vitamins and enzymes. Although small amounts of metal ions have protective properties, excess metal levels result in oxidative injury, which is why metal ion homeostasis is crucial for the proper functioning of the brain. The changes of their level in the brain have been proven to be a risk factor for Alzheimer's, Parkinson's, and Huntington's diseases, as well as amyotrophic lateral sclerosis. Therefore, it is currently an important application of various analytical methods. This review covers the most important of them: inductively coupled ground mass spectrometry (ICP-MS), flame-induced atomic absorption spectrometry (FAAS), electrothermal atomic absorption spectrometry (GFAAS), optical emission spectrometry with excitation in inductively coupled plasma (ICP-OES), X-ray fluorescence spectrometry (XRF), and neutron activation analysis (NAA). Additionally, we present a summary of concentration values found by different research groups.

Emerging chemical tools and techniques for tracking biological manganese

This frontier article discusses chemical tools and techniques for tracking and imaging Mn ions in biology.

True one cell chemical analysis: a review

The constantly growing field of True One Cell (TOC) analysis has provided important information on the direct chemical composition of various cells and cellular components.

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.

Catalyst discovery through megalibraries of nanomaterials

The nanomaterial landscape is so vast that a high-throughput combinatorial approach is required to understand structure-function relationships. To address this challenge, an approach for the synthesis and screening of megalibraries of unique nanoscale features (>10,000,000) with tailorable location, size, and composition has been developed. Polymer pen lithography, a parallel lithographic technique, is combined with an ink spray-coating method to create pen arrays, where each pen has a different but deliberately chosen quantity and composition of ink. With this technique, gradients of Au-Cu bimetallic nanoparticles have been synthesized and then screened for activity by in situ Raman spectroscopy with respect to single-walled carbon nanotube (SWNT) growth. Au₃Cu, a composition not previously known to catalyze SWNT growth, has been identified as the most active composition.

Iron and Copper Intracellular Chelation as an Anticancer Drug Strategy

A very promising direction in the development of anticancer drugs is inhibiting the molecular pathways that keep cancer cells alive and able to metastasize. Copper and iron are two essential metals that play significant roles in the rapid proliferation of cancer cells and several chelators have been studied to suppress the bioavailability of these metals in the cells. This review discusses the major contributions that Cu and Fe play in the progression and spreading of cancer and evaluates select Cu and Fe chelators that demonstrate great promise as anticancer drugs. Efforts to improve the cellular delivery, efficacy, and tumor responsiveness of these chelators are also presented including a transmetallation strategy for dual targeting of Cu and Fe. To elucidate the effectiveness and specificity of Cu and Fe chelators for treating cancer, analytical tools are described for measuring Cu and Fe levels and for tracking the metals in cells, tissue, and the body.

Iron and Copper Intracellular Chelation as an Anticancer Drug Strategy

A very promising direction in the development of anticancer drugs is inhibiting the molecular pathways that keep cancer cells alive and able to metastasize. Copper and iron are two essential metals that play significant roles in the rapid proliferation of cancer cells and several chelators have been studied to suppress the bioavailability of these metals in the cells. This review discusses the major contributions that Cu and Fe play in the progression and spreading of cancer and evaluates select Cu and Fe chelators that demonstrate great promise as anticancer drugs. Efforts to improve the cellular delivery, efficacy, and tumor responsiveness of these chelators are also presented including a transmetallation strategy for dual targeting of Cu and Fe. To elucidate the effectiveness and specificity of Cu and Fe chelators for treating cancer, analytical tools are described for measuring Cu and Fe levels and for tracking the metals in cells, tissue, and the body.

Correlative 3D x-ray fluorescence and ptychographic tomography of frozen-hydrated green algae

Accurate knowledge of elemental distributions within biological organisms is critical for understanding their cellular roles. The ability to couple this knowledge with overall cellular architecture in three dimensions (3D) deepens our understanding of cellular chemistry. Using a whole, frozen-hydrated Chlamydomonas reinhardtii cell as an example, we report the development of 3D correlative microscopy through a combination of simultaneous cryogenic x-ray ptychography and x-ray fluorescence microscopy. By taking advantage of a recently developed tomographic reconstruction algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), we produce high-quality 3D maps of the unlabeled alga's cellular ultrastructure and elemental distributions within the cell. We demonstrate GENFIRE's ability to outperform conventional tomography algorithms and to further improve the reconstruction quality by refining the experimentally intended tomographic angles. As this method continues to advance with brighter coherent light sources and more efficient data handling, we expect correlative 3D x-ray fluorescence and ptychographic tomography to be a powerful tool for probing a wide range of frozen-hydrated biological specimens, ranging from small prokaryotes such as bacteria, algae, and parasites to large eukaryotes such as mammalian cells, with applications that include understanding cellular responses to environmental stimuli and cell-to-cell interactions.

X-ray Fluorescence Nanotomography of Single Bacteria with a Sub-15 nm Beam

X-ray Fluorescence (XRF) microscopy is a growing approach for imaging the trace element concentration, distribution, and speciation in biological cells at the nanoscale. Moreover, three-dimensional nanotomography provides the added advantage of imaging subcellular structure and chemical identity in three dimensions without the need for staining or sectioning of cells. To date, technical challenges in X-ray optics, sample preparation, and detection sensitivity have limited the use of XRF nanotomography in this area. Here, XRF nanotomography was used to image the elemental distribution in individual E. coli bacterial cells using a sub-15 nm beam at the Hard X-ray Nanoprobe beamline (HXN, 3-ID) at NSLS-II. These measurements were simultaneously combined with ptychography to image structural components of the cells. The cells were embedded in small (3-20 µm) sodium chloride crystals, which provided a non-aqueous matrix to retain the three-dimensional structure of the E. coli while collecting data at room temperature. Results showed a generally uniform distribution of calcium in the cells, but an inhomogeneous zinc distribution, most notably with concentrated regions of zinc at the polar ends of the cells. This work demonstrates that simultaneous two-dimensional ptychography and XRF nanotomography can be performed with a sub-15 nm beam size on unfrozen biological cells to co-localize elemental distribution and nanostructure simultaneously.

Spatial distribution of metals within the liver acinus and their perturbation by PCB126

Animal studies show that exposure to the environmental pollutant 3,3',4,4',5-pentachlorobiphenyl (PCB126) causes alterations in hepatic metals as measured in acid-digested volume-adjusted tissue. These studies lack the detail of the spatial distribution within the liver. Here we use X-ray fluorescence microscopy (XFM) to assess the spatial distribution of trace elements within liver tissue. Liver samples from male Sprague Dawley rats, treated either with vehicle or PCB126, were formalin fixed and paraffin embedded. Serial sections were prepared for traditional H&E staining or placed on silicon nitride windows for XFM. With XFM, metal gradients between the portal triad and the central vein were seen, especially with copper and iron. These gradients change with exposure to PCB126, even reverse. This is the first report of how micronutrients vary spatially within the liver and how they change in response to toxicant exposure. In addition, high concentrations of zinc clusters were discovered in the extracellular space. PCB126 treatment did not affect their presence, but did alter their elemental makeup suggesting a more general biological function. Further work is needed to properly evaluate the gradients and their alterations as well as classify the zinc clusters to determine their role in liver function and zinc homeostasis.

Structure and Chemical Organization in Damselfly Calopteryx haemorrhoidalis Wings: A Spatially Resolved FTIR and XRF Analysis with Synchrotron Radiation

Insects represent the majority of known animal species and exploit a variety of fascinating nanotechnological concepts. We investigated the wings of the damselfly Calopteryx haemorrhoidalis, whose males have dark pigmented wings and females have slightly pigmented wings. We used scanning electron microscopy (SEM) and nanoscale synchrotron X-ray fluorescence (XRF) microscopy analysis for characterizing the nanostructure and the elemental distribution of the wings, respectively. The spatially resolved distribution of the organic constituents was examined by synchrotron Fourier transform infrared (s-FTIR) microspectroscopy and subsequently analyzed using hierarchical cluster analysis. The chemical distribution across the wing was rather uniform with no evidence of melanin in female wings, but with a high content of melanin in male wings. Our data revealed a fiber-like structure of the hairs and confirmed the presence of voids close to its base connecting the hairs to the damselfly wings. Within these voids, all detected elements were found to be locally depleted. Structure and elemental contents varied between wing membranes, hairs and veins. The elemental distribution across the membrane was rather uniform, with higher Ca, Cu and Zn levels in the male damselfly wing membranes.

Advanced Nuclear and Related Techniques for Metallomics and Nanometallomics

Metallomics, focusing on the global and systematic understanding of the metal uptake, trafficking, role, and excretion in biological systems, has attracted more and more attention. Metal-related nanomaterials, including metallic and metal-containing nanomaterials, have unique properties compared to their macroscale counterparts and therefore require special attention. The absorption, distribution, metabolism, excretion (ADME) behavior of metal-related nanomaterials in the biological systems is influenced by their physicochemical properties, the exposure route, and the microenvironment of the deposition site. Nanomaterials not only may interact directly or indirectly with genes, proteins, and other molecules to bring genotoxicity, immunotoxicity, DNA damage, and cytotoxicity but may also stimulate the immune responses, circumvent tumor resistance, and inhibit tumor metastasis. Because of their advantages of absolute quantification, high sensitivity, excellent accuracy and precision, low matrix effects, and nondestructiveness, nuclear and related analytical techniques have been playing important roles in the study of metallomics and nanometallomics. In this chapter, we present a comprehensive overview of nuclear and related analytical techniques applied to the quantification of metallome and nanometallome, the biodistribution, bioaccumulation, and transformation of metallome and nanometallome in vivo, and the structural analysis. Besides, metallomics and nanometallomics need to cooperate with other -omics, like genomics, proteomics, and metabolomics, to obtain the knowledge of underlying mechanisms and therefore to improve the application performance and to reduce the potential risk of metallome and nanometallome.

X-Ray Fluorescence-Detected Flow Cytometry

X-ray fluorescence-detected flow cytometry can enable the detection and characterization of ultra-trace, trace, and bulk elemental content at the cellular level using synchrotron-induced x-ray emission from fully aquated actively respiring cells. Although very much still a technique in development, this technique has been used to characterize cell-to-cell elemental variability in bovine red blood cells, Saccharomyces cerevisiae, and NIH3T3 mouse fibroblasts. Herein we describe the experimental setup and the key methodological aspects of data collection and processing.

The effect of metalloprotein inhibitors on cellular metal ion content and distribution

With metalloproteins garnering increased interest as therapeutic targets, designing target-specific metalloprotein inhibitors (MPi) is of substantial importance. However, in many respects, the development and evaluation of MPi lags behind that of conventional small molecule therapeutics. Core concerns around MPi, such as target selectivity and potential disruption of metal ion homeostasis linger. Herein, we used a suite of analytical methods, including energy-dispersive X-ray spectroscopy (EDX), inductively coupled plasma atomic emission spectroscopy (ICP-OES), and synchrotron X-ray fluorescence microscopy (SXRF) to investigate the effect of several MPi on cellular metal ion distribution and homeostasis. The results reveal that at therapeutically relevant concentrations, the tested MPi have no significant effects on cellular metal ion content or distribution. In addition, the affinity of the metal-binding pharmacophore (MBP) utilized by the MPi does not have a substantial influence on the effect of the MPi on cellular metal distribution. These studies provide an important, original data set indicating that metal ion homeostasis is not notably perturbed by MPi, which should encourage the development of and aid in designing new MPi, guide MBP selection, and clarify the effect of MPi on the 'metallome'.

MicroXRF tomographic visualization of zinc and iron in the zebrafish embryo at the onset of the hatching period

Transition metals such as zinc, copper, and iron play key roles in cellular proliferation, cell differentiation, growth, and development. Over the past decade, advances in synchrotron X-ray fluorescence instrumentation presented new opportunities for the three-dimensional mapping of trace metal distributions within intact specimens. Taking advantage of microXRF tomography, we visualized the 3D distribution of zinc and iron in a zebrafish embryo at the onset of the hatching period. The reconstructed volumetric data revealed distinct differences in the elemental distributions, with zinc predominantly localized to the yolk and yolk extension, and iron to various regions of the brain as well as the myotome extending along the dorsal side of the embryo. The data set complements an earlier tomographic study of an embryo at the pharyngula stage (24 hpf), thus offering new insights into the trace metal distribution at key stages of embryonic development.

Lensless Tomographic Imaging of Near Surface Structures of Frozen Hydrated Malaria-Infected Human Erythrocytes by Coherent X-Ray Diffraction Microscopy

Lensless, coherent X-ray diffraction microscopy has been drawing considerable attentions for tomographic imaging of whole human cells. In this study, we performed cryogenic coherent X-ray diffraction imaging of human erythrocytes with and without malaria infection. To shed light on structural features near the surface, “ghost cells” were prepared by the removal of cytoplasm. From two-dimensional images, we found that the surface of erythrocytes after 32 h of infection became much rougher compared to that of healthy, uninfected erythrocytes. The Gaussian roughness of an infected erythrocyte surface (69 nm) is about two times larger than that of an uninfected one (31 nm), reflecting the formation of protein knobs on infected erythrocyte surfaces. Three-dimensional tomography further enables to obtain images of the whole cells with no remarkable radiation damage, whose accuracy was estimated using phase retrieval transfer functions to be as good as 64 nm for uninfected and 80 nm for infected erythrocytes, respectively. Future improvements in phase retrieval algorithm, increase in degree of coherence, and higher flux in combination with complementary X-ray fluorescence are necessary to gain both structural and chemical details of mesoscopic architectures, such as cytoskeletons, membraneous structures, and protein complexes, in frozen hydrated human cells, especially under diseased states.

Imaging of neuronal tissues by x-ray diffraction and x-ray fluorescence microscopy: evaluation of contrast and biomarkers for neurodegenerative diseases

We have used scanning X-ray diffraction (XRD) and X-ray fluorescence (XRF) with micro-focused synchrotron radiation to study histological sections from human substantia nigra (SN). Both XRF and XRD mappings visualize tissue properties, which are inaccessible by conventional microscopy and histology. We propose to use these advanced tools to characterize neuronal tissue in neurodegeneration, in particular in Parkinson's disease (PD). To this end, we take advantage of the recent experimental progress in x-ray focusing, detection, and use automated data analysis scripts to enable quantitative analysis of large field of views. XRD signals are recorded and analyzed both in the regime of small-angle (SAXS) and wide-angle x-ray scattering (WAXS). The SAXS signal was analyzed in view of the local myelin structure, while WAXS was used to identify crystalline deposits. PD tissue scans exhibited increased amounts of crystallized cholesterol. The XRF analysis showed increased amounts of iron and decreased amounts of copper in the PD tissue compared to the control.

Quantitative IR microscopy and spectromics open the way to 3D digital pathology

Currently, only mass-spectrometry (MS) microscopy brings a quantitative analysis of chemical contents of tissue samples in 3D. Here, the reconstruction of a 3D quantitative chemical images of a biological tissue by FTIR spectro-microscopy is reported. An automated curve-fitting method is developed to extract all intense absorption bands constituting IR spectra. This innovation benefits from three critical features: (1) the correction of raw IR spectra to make them quantitatively comparable; (2) the automated and iterative data treatment allowing to transfer the IR-absorption spectrum into a IR-band spectrum; (3) the reconstruction of an 3D IR-band matrix (x, y, z for voxel position and a 4^th dimension with all IR-band parameters). Spectromics, which is a new method for exploiting spectral data for tissue metadata reconstruction, is proposed to further translate the related chemical information in 3D, as biochemical and anatomical tissue parameters. An example is given with oxidative stress distribution and the reconstruction of blood vessels in tissues. The requirements of IR microscopy instrumentation to propose 3D digital histology as a clinical routine technology is briefly discussed.

Combined scanning X-ray diffraction and holographic imaging of cardiomyocytes

This article presents scanning small-angle X-ray scattering (SAXS) experiments on the actomyosin assemblies in freeze-dried neo-natal rat cardiac muscle cells. By scanning the cells through a sub-micrometre focused beam, the local structure and filament orientation can be probed and quantified. To this end, SAXS data were recorded and analyzed directly in reciprocal space to generate maps of different structural parameters (scanning SAXS). The scanning SAXS experiments were complemented by full-field holographic imaging of the projected electron density, following a slight rearrangement of the instrumental setup. It is shown that X-ray holography is ideally suited to complete missing scattering data at low momentum transfer in the structure factor, extending the covered range of spatial frequencies by two orders of magnitude. Regions of interest for scanning can be easily selected on the basis of the electron density maps. Finally, the combination of scanning SAXS and holography allows for a direct verification of possible radiation-induced structural changes in the cell.

X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning

X-ray microscopy can be used to image whole, unsectioned cells in their native hydrated state. It complements the higher resolution of electron microscopy for submicrometer thick specimens, and the molecule-specific imaging capabilites of fluorescence light microscopy. We describe here the first use of fast, continuous x-ray scanning of frozen hydrated cells for simultaneous sub-20 nm resolution ptychographic transmission imaging with high contrast, and sub-100 nm resolution deconvolved x-ray fluorescence imaging of diffusible and bound ions at native concentrations, without the need to add specific labels. By working with cells that have been rapidly frozen without the use of chemical fixatives, and imaging them under cryogenic conditions, we are able to obtain images with well preserved structural and chemical composition, and sufficient stability against radiation damage to allow for multiple images to be obtained with no observable change.

µ-XRF Studies on the Colour Brilliance in Ancient Wool Carpets

Many handmade ancient and recent oriental wool carpets show outstanding brilliance and persistence of colour that is not achieved by common industrial dyeing procedures. Anthropologists have suggested the influence of wool fermentation prior to dyeing as key technique to achieve the high dyeing quality. By means of μ-XRF elemental mapping of mordant metals we corroborate this view and show a deep and homogenous penetration of colourants into fermented wool fibres. Furthermore we are able to apply this technique and prove that the fermentation process for ancient specimens cannot be investigated by standard methods due to the lack of intact cuticle layers. This finding suggests a broad range of further investigations that will contribute to a deeper understanding of the development of traditional dyeing techniques. Spectroscopic studies add information on the oxidation states of the metal ions within the respective mordant-dye-complexes and suggest a partial charge transfer as basis for a significant colour change when Fe mordants are used.