Non-negative matrix factorization for the near real-time interpretation of absorption effects in elemental distribution images acquired by X-ray fluorescence imaging.

Elemental distribution images acquired by imaging X-ray fluorescence analysis can contain high degrees of redundancy and weakly discernible correlations. In this article near real-time non-negative matrix factorization (NMF) is described for the analysis of a number of data sets acquired from samples of a bi-modal α+ß Ti-6Al-6V-2Sn alloy. NMF was used for the first time to reveal absorption artefacts in the elemental distribution images of the samples, where two phases of the alloy, namely α and ß, were in superposition. The findings and interpretation of the NMF results were confirmed by Monte Carlo simulation of the layered alloy system. Furthermore, it is shown how the simultaneous factorization of several stacks of elemental distribution images provides uniform basis vectors and consequently simplifies the interpretation of the representation.

Speciation and distribution of arsenic in the nonhyperaccumulator macrophyte Ceratophyllum demersum.

Although arsenic (As) is a common pollutant worldwide, many questions about As metabolism in nonhyperaccumulator plants remain. Concentration- and tissue-dependent speciation and distribution of As was analyzed in the aquatic plant Ceratophyllum demersum to understand As metabolism in nonhyperaccumulator plants. Speciation was analyzed chromatographically (high-performance liquid chromatography-[inductively coupled plasma-mass spectrometry]-[electrospray ionization-mass spectrometry]) in whole-plant extracts and by tissue-resolution confocal x-ray absorption near-edge spectroscopy in intact shock-frozen hydrated leaves, which were also used for analyzing cellular element distribution through x-ray fluorescence. Chromatography revealed up to 20 As-containing species binding more than 60% of accumulated As. Of these, eight were identified as thiol-bound (phytochelatins [PCs], glutathione, and cysteine) species, including three newly identified complexes: Cys-As(III)-PC2, Cys-As-(GS)2, and GS-As(III)-desgly-PC2. Confocal x-ray absorption near-edge spectroscopy showed arsenate, arsenite, As-(GS)3, and As-PCs with varying ratios in various tissues. The epidermis of mature leaves contained the highest proportion of thiol (mostly PC)-bound As, while in younger leaves, a lower proportion of As was thiol bound. At higher As concentrations, the percentage of unbound arsenite increased in the vein and mesophyll of young mature leaves. At the same time, x-ray fluorescence showed an increase of total As in the vein and mesophyll but not in the epidermis of young mature leaves, while this was reversed for zinc distribution. Thus, As toxicity was correlated with a change in As distribution pattern and As species rather than a general increase in many tissues.

Kinoform diffractive lenses for efficient nano-focusing of hard X-rays.

A nano-focusing module based on two linear Fresnel zone plates is presented. The zone plates are designed to generate a kinoform phase profile in tilted geometry, thus overcoming the efficiency limitations of binary diffractive structures. Adjustment of the tilt angle enables tuning of the setup for optimal efficiency over a wide range of photon energies, ranging from 5 to 20 keV. Diffraction efficiency of more than 50% was measured for the full module at 8 keV photon energy. A diffraction limited spot size of 100 nm was verified by ptychographic reconstruction for a lens module with a large entrance aperture of 440 µm × 400 µm.

Synchrotron X-rays reveal the modes of Fe binding and trace metal storage in the brown algae Laminaria digitata and Ectocarpus siliculosus.

Iron is accumulated symplastically in kelp in a non-ferritin core that seems to be a general feature of brown algae. Microprobe studies show that Fe binding depends on tissue type. The sea is generally an iron-poor environment and brown algae were recognized in recent years for having a unique, ferritin-free iron storage system. Kelp (Laminaria digitata) and the filamentous brown alga Ectocarpus siliculosus were investigated using X-ray microprobe imaging and nanoprobe X-ray fluorescence tomography to explore the localization of iron, arsenic, strontium, and zinc, and micro-X-ray absorption near-edge structure (µXANES) to study Fe binding. Fe distribution in frozen hydrated environmental samples of both algae shows higher accumulation in the cortex with symplastic subcellular localization. This should be seen in the context of recent ultrastructural insight by cryofixation-freeze substitution that found a new type of cisternae that may have a storage function but differs from the apoplastic Fe accumulation found by conventional chemical fixation. Zn distribution co-localizes with Fe in E. siliculosus, whereas it is chiefly located in the L. digitata medulla, which is similar to As and Sr. Both As and Sr are mostly found at the cell wall of both algae. XANES spectra indicate that Fe in L. digitata is stored in a mineral non-ferritin core, due to the lack of ferritin-encoding genes. We show that the L. digitata cortex contains mostly a ferritin-like mineral, while the meristoderm may include an additional component.

Structure-function relationship in an archaebacterial methionine sulphoxide reductase B.

Oxidation of methionine to methionine sulphoxide (MetSO) may lead to loss of molecular integrity and function. This oxidation can be 'repaired' by methionine sulphoxide reductases (MSRs), which reduce MetSO back to methionine. Two structurally unrelated classes of MSRs, MSRA and MSRB, show stereoselectivity towards the S and the R enantiomer of the sulphoxide respectively. Interestingly, these enzymes were even maintained throughout evolution in anaerobic organisms. Here, the activity and the nuclear magnetic resonance (NMR) structure of MTH711, a zinc containing MSRB from the thermophilic, methanogenic archaebacterium Methanothermobacter thermoautotrophicus, are described. The structure appears more rigid as compared with similar MSRBs from aerobic and mesophilic organisms. No significant structural differences between the oxidized and the reduced MTH711 state can be deduced from our NMR data. A stable sulphenic acid is formed at the catalytic Cys residue upon oxidation of the enzyme with MetSO. The two non-zinc-binding cysteines outside the catalytic centre are not necessary for activity of MTH711 and are not situated close enough to the active-site cysteine to serve in regenerating the active centre via the formation of an intramolecular disulphide bond. These findings imply a reaction cycle that differs from that observed for other MSRBs.

Towards a black-box for biological EXAFS data analysis. II. Automatic BioXAS Refinement and Analysis (ABRA).

In biological systems, X-ray absorption spectroscopy (XAS) can determine structural details of metal binding sites with high resolution. Here a method enabling an automated analysis of the corresponding EXAFS data is presented, utilizing in addition to least-squares refinement the prior knowledge about structural details and important fit parameters. A metal binding motif is characterized by the type of donor atoms and their bond lengths. These fit results are compared by bond valance sum analysis and target distances with established structures of metal binding sites. Other parameters such as the Debye-Waller factor and shift of the Fermi energy provide further insights into the quality of a fit. The introduction of mathematical criteria, their combination and calibration allows an automated analysis of XAS data as demonstrated for a number of examples. This presents a starting point for future applications to all kinds of systems studied by XAS and allows the algorithm to be transferred to data analysis in other fields.

The ligand environment of zinc stored in vesicles.

Zinc serves regulatory functions in cells and thus, several mechanisms exist for tight control of its homeostasis. One mechanism is storage in and retrieval from vesicles, so-called zincosomes, but the chemical speciation of zincosomal zinc has remained enigmatic. Here, we determine the intravesicular zinc-coordination in isolated zincosomes in comparison to intact RAW264.7 murine macrophage cells. In elemental maps of a cell monolayer, generated by microbeam X-ray fluorescence, zincosomes were identified as spots of high zinc accumulation. A fingerprint for the binding motif obtained by muXANES (X-ray absorption near edge structure) matches the XANES from isolated vesicles; zinc is not free, but present as a complexed form (average coordination; 1.0 sulfur, 2,5 histidines 30 and 1.0 oxygen), resembling regulatory or catalytic zinc sites in proteins. Such coordination enables reversible binding, acting as a 'zinc sink', facilitating the accumulation of high amounts of zinc against a concentration gradient.

Fast Strain Mapping of Nanowire Light-Emitting Diodes Using Nanofocused X-ray Beams.

X-ray nanobeams are unique nondestructive probes that allow direct measurements of the nanoscale strain distribution and composition inside the micrometer thick layered structures that are found in most electronic device architectures. However, the method is usually extremely time-consuming, and as a result, data sets are often constrained to a few or even single objects. Here we demonstrate that by special design of a nanofocused X-ray beam diffraction experiment we can (in a single 2D scan with no sample rotation) measure the individual strain and composition profiles of many structures in an array of upright standing nanowires. We make use of the observation that in the generic nanowire device configuration, which is found in high-speed transistors, solar cells, and light-emitting diodes, each wire exhibits very small degrees of random tilts and twists toward the substrate. Although the tilt and twist are very small, they give a new contrast mechanism between different wires. In the present case, we image complex nanowires for nanoLED fabrication and compare to theoretical simulations, demonstrating that this fast method is suitable for real nanostructured devices.

Effects of nanomolar copper on water plants--comparison of biochemical and biophysical mechanisms of deficiency and sublethal toxicity under environmentally relevant conditions.

Toxicity and deficiency of essential trace elements like Cu are major global problems. Here, environmentally relevant sub-micromolar concentrations of Cu (supplied as CuSO4) and simulations of natural light- and temperature cycles were applied to the aquatic macrophyte Ceratophyllum demersum. Growth was optimal at 10nM Cu, while PSII activity (Fv/Fm) was maximal around 2 nM Cu. Damage to the PSII reaction centre was the first target of Cu toxicity, followed by disturbed regulation of heat dissipation (NPQ). Only after that, electron transport through PSII (ΦPSII) was inhibited, and finally chlorophylls decreased. Copper accumulation in the plants was stable until 10nM Cu in solution, but strongly increased at higher concentrations. The vein was the main storage site for Cu up to physiological concentrations (10nM). At toxic levels it was also sequestered to the epidermis and mesophyll until export from the vein became inhibited, accompanied by inhibition of Zn uptake. Copper deficiency led to a complete stop of growth at "0"nM Cu after 6 weeks. This was accompanied by high starch accumulation although electron flow through PSII (ΦPSII) decreased from 2 weeks, followed by decrease in pigments and increase of non photochemical quenching (NPQ). Release of Cu from the plants below 10nM Cu supply in the nutrient solution indicated lack of high-affinity Cu transporters, and on the tissue level copper deficiency led to a re-distribution of zinc.

Different strategies of cadmium detoxification in the submerged macrophyte Ceratophyllum demersum L.

The heavy metal cadmium (Cd) is highly toxic to plants. To understand the mechanisms of tolerance and resistance to Cd, we treated the rootless, submerged macrophyte Ceratophyllum demersum L. with sub-micromolar concentrations of Cd under environmentally relevant conditions. X-ray fluorescence measurements revealed changing distribution patterns of Cd and Zn at non-toxic (0.2 nM, 2 nM), moderately toxic (20 nM) and highly toxic (200 nM) levels of Cd. Increasing Cd concentrations led to enhanced sequestration of Cd into non-photosynthetic tissues like epidermis and vein. At toxic Cd concentrations, Zn was redistributed and mainly found in the vein. Cd treatment induced the synthesis of phytochelatins (PCs) in the plants, with a threshold of induction already at 20 nM Cd for PC3. In comparison, in plants treated with Cu, elevated PC levels were detected only at the highest concentrations (100-200 nM Cu). Our results show that also non-accumulators like C. demersum store toxic metals in tissues where the heavy metal interferes least with metabolic pathways, but remaining toxicity interferes with micronutrient distribution. Furthermore, we found that the induction of phytochelatins is not proportional to metal concentration, but has a distinct threshold, specific for each PC species. Finally we could show that 20 nM Cd, which was previously regarded as non-toxic to most plants, already induces detoxifying mechanisms.

Avian magnetoreception: elaborate iron mineral containing dendrites in the upper beak seem to be a common feature of birds.

The magnetic field sensors enabling birds to extract orientational information from the Earth's magnetic field have remained enigmatic. Our previously published results from homing pigeons have made us suggest that the iron containing sensory dendrites in the inner dermal lining of the upper beak are a candidate structure for such an avian magnetometer system. Here we show that similar structures occur in two species of migratory birds (garden warbler, Sylvia borin and European robin, Erithacus rubecula) and a non-migratory bird, the domestic chicken (Gallus gallus). In all these bird species, histological data have revealed dendrites of similar shape and size, all containing iron minerals within distinct subcellular compartments of nervous terminals of the median branch of the Nervus ophthalmicus. We also used microscopic X-ray absorption spectroscopy analyses to identify the involved iron minerals to be almost completely Fe III-oxides. Magnetite (Fe II/III) may also occur in these structures, but not as a major Fe constituent. Our data suggest that this complex dendritic system in the beak is a common feature of birds, and that it may form an essential sensory basis for the evolution of at least certain types of magnetic field guided behavior.

The two distinctive metal ion binding domains of the wheat metallothionein Ec-1.

Metallothioneins are small cysteine-rich proteins believed to play a role, among others, in the homeostasis of essential metal ions such as Zn(II) and Cu(I). Recently, we could show that wheat E(c)-1 is coordinating its six Zn(II) ions in form of metal-thiolate clusters analogously to the vertebrate metallothioneins. Specifically, two Zn(II) ions are bound in the N-terminal and four in the C-terminal domain. In the following, we will present evidence for the relative independence of the two domains from each other with respect to their metal ion binding abilities, and uncover three intriguing peculiarities of the protein. Firstly, one Zn(II) ion of the N-terminal domain is relative resistant to complete replacement with Cd(II) indicating the presence of a Zn(II)-binding site with increased stability. Secondly, the C-terminal domain is able to coordinate an additional fifth metal ion, though with reduced affinity, which went undetected so far. Finally, reconstitution of apoE(c)-1 with an excess of Zn(II) shows a certain amount of sub-stoichiometrically metal-loaded species. The possible relevance of these finding for the proposed biological functions of wheat E(c)-1 will be discussed. In addition, extended X-ray absorption fine structure (EXAFS) measurements on both, the full-length and the truncated protein, provide final evidence for His participation in metal ion binding.

Iron-sulfur repair YtfE protein from Escherichia coli: structural characterization of the di-iron center.

YtfE was recently shown to be a newly discovered protein required for the recovery of the activity of iron-sulfur-containing enzymes damaged by oxidative and nitrosative stress conditions. The Escherichia coli YtfE purified protein is a dimer with two iron atoms per monomer and the type and properties of the iron center were investigated by using a combination of resonance Raman and extended X-ray absorption fine structure spectroscopies. The results demonstrate that YtfE contains a non-heme dinuclear iron center having mu-oxo and mu-carboxylate bridging ligands and six histidine residues coordinating the iron ions. This is the first example of a protein from this important class of di-iron proteins to be shown to be involved in the repair of iron-sulfur centers.