3D chemical mapping: application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences

Analysis of Cr(VI) Bioremediation by Citrobacter freundii Using Synchrotron Soft X-ray Scanning Transmission X-ray Microscopy

Scanning transmission X-ray microscopy (STXM) was utilized for analysing the bioremediation of Cr(VI) by Citrobacter freundii, a species of gram-negative bacteria. The biosorption and bioreduction processes were analysed by the chemical mapping of cells biosorbed at different concentrations of Cr(VI). STXM spectromicroscopy images were recorded at O K-edge and Cr L-edge. A thorough analysis of the X-ray absorption features corresponding to different oxidation states of Cr in the biosorbed cell indicated the coexistence of Cr(III) and Cr(VI) at higher concentrations. This signifies the presence of partially reduced Cr(VI) in addition to biosorbed Cr(VI). In addition, the Cr(III) signal is intense compared with Cr(VI) at different regions of the cell indicating excess of reduced Cr. Speciation of adsorbed Cr was analysed for the spectral features of biosorbed cell and comparison with Cr standards. Analysis of absorption onset, L3/L2 ratio and absorption fine structure concludes that adsorbed Cr is predominantly present as Cr(III) hydroxide or oxyhydroxide. The evolution of absorption features in the duration of biosorption process was also studied. These time lapse studies depict the gradual decrement in Cr(VI) signal as biosorption proceeds. A strong evidence of interaction of Cr with the cell material was also observed. The obtained results provide insights into the biosorption process and chemical speciation of Cr on the cells.

Differential electron yield imaging with STXM

Total electron yield (TEY) imaging is an established scanning transmission X-ray microscopy (STXM) technique that gives varying contrast based on a sample's geometry, elemental composition, and electrical conductivity. However, the TEY-STXM signal is determined solely by the electrons that the beam ejects from the sample. A related technique, X-ray beam-induced current (XBIC) imaging, is sensitive to electrons and holes independently, but requires electric fields in the sample. Here we report that multi-electrode devices can be wired to produce differential electron yield (DEY) contrast, which is also independently sensitive to electrons and holes, but does not require an electric field. Depending on whether the region illuminated by the focused STXM beam is better connected to one electrode or another, the DEY-STXM contrast changes sign. DEY-STXM images thus provide a vivid map of a device's connectivity landscape, which can be key to understanding device function and failure. To demonstrate an application in the area of failure analysis, we image a 100 nm, lithographically-defined aluminum nanowire that has failed after being stressed with a large current density.

Across the spectrum: integrating multidimensional metal analytics for in situ metallomic imaging

To know how much of a metal species is in a particular location within a biological context at any given time is essential for understanding the intricate roles of metals in biology and is the fundamental question upon which the field of metallomics was born. Simply put, seeing is powerful. With the combination of spectroscopy and microscopy, we can now see metals within complex biological matrices complemented by information about associated molecules and their structures. With the addition of mass spectrometry and particle beam based techniques, the field of view grows to cover greater sensitivities and spatial resolutions, addressing structural, functional and quantitative metallomic questions from the atomic level to whole body processes. In this perspective, I present a paradigm shift in the way we relate to and integrate current and developing metallomic analytics, highlighting both familiar and perhaps less well-known state of the art techniques for in situ metallomic imaging, specific biological applications, and their use in correlative studies. There is a genuine need to abandon scientific silos and, through the establishment of a metallomic scientific platform for further development of multidimensional analytics for in situ metallomic imaging, we have an incredible opportunity to enhance the field of metallomics and demonstrate how discovery research can be done more effectively.

Imaging cell morphology and physiology using X-rays

Morphometric measurements, such as quantifying cell shape, characterizing sub-cellular organization, and probing cell-cell interactions, are fundamental in cell biology and clinical medicine. Until quite recently, the main source of morphometric data on cells has been light- and electron-based microscope images. However, many technological advances have propelled X-ray microscopy into becoming another source of high-quality morphometric information. Here, we review the status of X-ray microscopy as a quantitative biological imaging modality. We also describe the combination of X-ray microscopy data with information from other modalities to generate polychromatic views of biological systems. For example, the amalgamation of molecular localization data, from fluorescence microscopy or spectromicroscopy, with structural information from X-ray tomography. This combination of data from the same specimen generates a more complete picture of the system than that can be obtained by a single microscopy method. Such multimodal combinations greatly enhance our understanding of biology by combining physiological and morphological data to create models that more accurately reflect the complexities of life.

Scanning transmission X-ray microscopy with efficient X-ray fluorescence detection (STXM-XRF) for biomedical applications in the soft and tender energy range

Scanning transmission X-ray microscopy, especially in combination with X-ray fluorescence detection (STXM-XRF) in the soft X-ray energy range, is becoming an increasingly important tool for life sciences. Using X-ray fluorescence detection, the study of biochemical mechanisms becomes accessible. As biological matrices generally have a low fluorescence yield and thus a low fluorescence signal, high detector efficiency (e.g. large solid angle) is indispensable for avoiding long measurement times and radiation damage. Here, the new AnImaX STXM-XRF microscope equipped with a large solid angle of detection enabling fast scans and the first proof-of-principle measurements on biomedical samples are described. In addition, characterization measurements for future quantitative elemental imaging are presented.

Optimization of Three-Dimensional (3D) Chemical Imaging by Soft X-Ray Spectro-Tomography Using a Compressed Sensing Algorithm

Soft X-ray spectro-tomography provides three-dimensional (3D) chemical mapping based on natural X-ray absorption properties. Since radiation damage is intrinsic to X-ray absorption, it is important to find ways to maximize signal within a given dose. For tomography, using the smallest number of tilt series images that gives a faithful reconstruction is one such method. Compressed sensing (CS) methods have relatively recently been applied to tomographic reconstruction algorithms, providing faithful 3D reconstructions with a much smaller number of projection images than when conventional reconstruction methods are used. Here, CS is applied in the context of scanning transmission X-ray microscopy tomography. Reconstructions by weighted back-projection, the simultaneous iterative reconstruction technique, and CS are compared. The effects of varying tilt angle increment and angular range for the tomographic reconstructions are examined. Optimization of the regularization parameter in the CS reconstruction is explored and discussed. The comparisons show that CS can provide improved reconstruction fidelity relative to weighted back-projection and simultaneous iterative reconstruction techniques, with increasingly pronounced advantages as the angular sampling is reduced. In particular, missing wedge artifacts are significantly reduced and there is enhanced recovery of sharp edges. Examples of using CS for low-dose scanning transmission X-ray microscopy spectroscopic tomography are presented.

Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell-Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria

Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.

Overview of nanoscale NEXAFS performed with soft X-ray microscopes

Today, in material science nanoscale structures are becoming more and more important. Not only for the further miniaturization of semiconductor devices like carbon nanotube based transistors, but also for newly developed efficient energy storage devices, gas sensors or catalytic systems nanoscale and functionalized materials have to be analysed. Therefore, analytical tools like near-edge X-ray absorption fine structure (NEXAFS) spectroscopy has to be applied on single nanostructures. Scanning transmission X-ray microscopes (STXM) as well as full-field transmission X-ray microscopes (TXM) allow the required spatial resolution to study individual nanostructures. In the soft X-ray energy range only STXM was used so far for NEXAFS studies. Due to its unique setup, the TXM operated by the Helmholtz-Zentrum Berlin (HZB) at the electron storage ring BESSY II is the first one in the soft X-ray range which can be used for NEXAFS spectroscopy studies which will be shown in this review. Here we will give an overview of the different microscopes used for NEXAFS studies and describe their advantages and disadvantages for different samples.

Nano-scale spatial assessment of calcium distribution in coccolithophores using synchrotron-based nano-CT and STXM-NEXAFS

Calcified coccolithophores generate calcium carbonate scales around their cell surface. In light of predicted climate change and the global carbon cycle, the biomineralization ability of coccoliths has received growing interest. However, the underlying biomineralization mechanism is not yet well understood; the lack of non-invasive characterizing tools to obtain molecular level information involving biogenic processes and biomineral components remain significant challenges. In the present study, synchrotron-based Nano-computed Tomography (Nano-CT) and Scanning Transmission X-ray Microscopy-Near-edge X-ray Absorption Fine Structure Spectromicroscopy (STXM-NEXAFS) techniques were employed to identify Ca spatial distribution and investigate the compositional chemistry and distinctive features of the association between biomacromolecules and mineral components of calcite present in coccoliths. The Nano-CT results show that the coccolith scale vesicle is similar as a continuous single channel. The mature coccoliths were intracellularly distributed and immediately ejected and located at the exterior surface to form a coccoshpere. The NEXAFS spectromicroscopy results of the Ca L edge clearly demonstrate the existence of two levels of gradients spatially, indicating two distinctive forms of Ca in coccoliths: a crystalline-poor layer surrounded by a relatively crystalline-rich layer. The results show that Sr is absorbed by the coccoliths and that Sr/Ca substitution is rather homogeneous within the coccoliths. Our findings indicate that synchrotron-based STXM-NEXAFS and Nano-CT are excellent tools for the study of biominerals and provide information to clarify biomineralization mechanism.

Three-dimensional mid-infrared tomographic imaging of endogenous and exogenous molecules in a single intact cell with subcellular resolution

Microscopy in the mid-infrared spectral range provides detailed chemical information on a sample at moderate spatial resolution and is being used increasingly in the characterization of biological entities as challenging as single cells. However, a conventional cellular 2D imaging measurement is limited in its ability to associate specific compositional information to subcellular structures because of the interference from the complex topography of the sample. Herein we provide a method and protocols that overcome this challenge in which tilt-series infrared tomography is used with a standard benchtop infrared microscope. This approach gives access to the quantitative 3D distribution of molecular components based on the intrinsic contrast provided by the sample. We demonstrate the method by quantifying the distribution of an exogenous metal carbonyl complex throughout the cell and by reporting changes in its coordination sphere in different locations in the cell.

The role of iron in neurodegenerative disorders: insights and opportunities with synchrotron light

There is evidence for iron dysregulation in many forms of disease, including a broad spectrum of neurodegenerative disorders. In order to advance our understanding of the pathophysiological role of iron, it is helpful to be able to determine in detail the distribution of iron as it relates to metabolites, proteins, cells, and tissues, the chemical state and local environment of iron, and its relationship with other metal elements. Synchrotron light sources, providing primarily X-ray beams accompanied by access to longer wavelengths such as infra-red, are an outstanding tool for multi-modal non-destructive analysis of iron in these systems. The micro- and nano-focused X-ray beams that are generated at synchrotron facilities enable measurement of iron and other transition metal elements to be performed with outstanding analytic sensitivity and specificity. Recent developments have increased the scope for methods such as X-ray fluorescence mapping to be used quantitatively rather than semi-quantitatively. Burgeoning interest, coupled with technical advances and beamline development at synchrotron facilities, has led to substantial improvements in resources and methodologies in the field over the past decade. In this paper we will consider how the field has evolved with regard to the study of iron in proteins, cells, and brain tissue, and identify challenges in sample preparation and analysis. Selected examples will be used to illustrate the contribution, and future potential, of synchrotron X-ray analysis for the characterization of iron in model systems exhibiting iron dysregulation, and for human cases of neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, Friedreich's ataxia, and amyotrophic lateral sclerosis.