Sirine C. Fakra

Interferometer-controlled scanning transmission X-ray microscopes at the Advanced Light Source

Two new soft X-ray scanning transmission microscopes located at the Advanced Light Source (ALS) have been designed, built and commissioned. Interferometer control implemented in both microscopes allows the precise measurement of the transverse position of the zone plate relative to the sample. Long-term positional stability and compensation for transverse displacement during translations of the zone plate have been achieved. The interferometer also provides low-distortion orthogonal x, y imaging. Two different control systems have been developed: a digital control system using standard VXI components at beamline 7.0, and a custom feedback system based on PC AT boards at beamline 5.3.2. Both microscopes are diffraction limited with the resolution set by the quality of the zone plates. Periodic features with 30 nm half period can be resolved with a zone plate that has a 40 nm outermost zone width. One microscope is operating at an undulator beamline (7.0), while the other is operating at a novel dedicated bending-magnet beamline (5.3.2), which is designed specifically to illuminate the microscope. The undulator beamline provides count rates of the order of tens of MHz at high-energy resolution with photon energies of up to about 1000 eV. Although the brightness of a bending-magnet source is about four orders of magnitude smaller than that of an undulator source, photon statistics limited operation with intensities in excess of 3 MHz has been achieved at high energy resolution and high spatial resolution. The design and performance of these microscopes are described.

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalks metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2 μm h−1). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100 nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.

Elemental compositions of comet 81P/Wild 2 samples collected by Stardust

We measured the elemental compositions of material from 23 particles in aerogel and from residue in seven craters in aluminum foil that was collected during passage of the Stardust spacecraft through the coma of comet 81P/Wild 2. These particles are chemically heterogeneous at the largest size scale analyzed (∼180 ng). The mean elemental composition of this Wild 2 material is consistent with the CI meteorite composition, which is thought to represent the bulk composition of the solar system, for the elements Mg, Si, Mn, Fe, and Ni to 35%, and for Ca and Ti to 60%. The elements Cu, Zn, and Ga appear enriched in this Wild 2 material, which suggests that the CI meteorites may not represent the solar system composition for these moderately volatile minor elements.

A dedicated superbend x-ray microdiffraction beamline for materials, geo-, and environmental sciences at the advanced light source

A new facility for microdiffraction strain measurements and microfluorescence mapping has been built on beamline 12.3.2 at the advanced light source of the Lawrence Berkeley National Laboratory. This beamline benefits from the hard x-radiation generated by a 6 T superconducting bending magnet (superbend). This provides a hard x-ray spectrum from 5 to 22 keV and a flux within a 1 microm spot of approximately 5x10(9) photons/s (0.1% bandwidth at 8 keV). The radiation is relayed from the superbend source to a focus in the experimental hutch by a toroidal mirror. The focus spot is tailored by two pairs of adjustable slits, which serve as secondary source point. Inside the lead hutch, a pair of Kirkpatrick-Baez (KB) mirrors placed in a vacuum tank refocuses the secondary slit source onto the sample position. A new KB-bending mechanism with active temperature stabilization allows for more reproducible and stable mirror bending and thus mirror focusing. Focus spots around 1 microm are routinely achieved and allow a variety of experiments, which have in common the need of spatial resolution. The effective spatial resolution (approximately 0.2 microm) is limited by a convolution of beam size, scan-stage resolution, and stage stability. A four-bounce monochromator consisting of two channel-cut Si(111) crystals placed between the secondary source and KB-mirrors allows for easy changes between white-beam and monochromatic experiments while maintaining a fixed beam position. High resolution stage scans are performed while recording a fluorescence emission signal or an x-ray diffraction signal coming from either a monochromatic or a white focused beam. The former allows for elemental mapping, whereas the latter is used to produce two-dimensional maps of crystal-phases, -orientation, -texture, and -strain/stress. Typically achieved strain resolution is in the order of 5x10(-5) strain units. Accurate sample positioning in the x-ray focus spot is achieved with a commercial laser-triangulation unit. A Si-drift detector serves as a high-energy-resolution (approximately 150 eV full width at half maximum) fluorescence detector. Fluorescence scans can be collected in continuous scan mode with up to 300 pixels/s scan speed. A charge coupled device area detector is utilized as diffraction detector. Diffraction can be performed in reflecting or transmitting geometry. Diffraction data are processed using XMAS, an in-house written software package for Laue and monochromatic microdiffraction analysis.

Molecular Mechanisms of Selenium Tolerance and Hyperaccumulation in Stanleya pinnata

The molecular mechanisms responsible for selenium (Se) tolerance and hyperaccumulation were studied in the Se hyperaccumulator Stanleya pinnata (Brassicaceae) by comparing it with the related secondary Se accumulator Stanleya albescens using a combination of physiological, structural, genomic, and biochemical approaches. S. pinnata accumulated 3.6-fold more Se and was tolerant to 20 μm selenate, while S. albescens suffered reduced growth, chlorosis and necrosis, impaired photosynthesis, and high levels of reactive oxygen species. Levels of ascorbic acid, glutathione, total sulfur, and nonprotein thiols were higher in S. pinnata, suggesting that Se tolerance may in part be due to increased antioxidants and up-regulated sulfur assimilation. S. pinnata had higher selenocysteine methyltransferase protein levels and, judged from liquid chromatography-mass spectrometry, mainly accumulated the free amino acid methylselenocysteine, while S. albescens accumulated mainly the free amino acid selenocystathionine. S. albescens leaf x-ray absorption near-edge structure scans mainly detected a carbon-Se-carbon compound (presumably selenocystathionine) in addition to some selenocysteine and selenate. Thus, S. albescens may accumulate more toxic forms of Se in its leaves than S. pinnata. The species also showed different leaf Se sequestration patterns: while S. albescens showed a diffuse pattern, S. pinnata sequestered Se in localized epidermal cell clusters along leaf margins and tips, concentrated inside of epidermal cells. Transcript analyses of S. pinnata showed a constitutively higher expression of genes involved in sulfur assimilation, antioxidant activities, defense, and response to (methyl)jasmonic acid, salicylic acid, or ethylene. The levels of some of these hormones were constitutively elevated in S. pinnata compared with S. albescens, and leaf Se accumulation was slightly enhanced in both species when these hormones were supplied. Thus, defense-related phytohormones may play an important signaling role in the Se hyperaccumulation of S. pinnata, perhaps by constitutively up-regulating sulfur/Se assimilation followed by methylation of selenocysteine and the targeted sequestration of methylselenocysteine.

The fate of ZnO nanoparticles administered to human bronchial epithelial cells.

A particular challenge for nanotoxicology is the evaluation of the biological fate and toxicity of nanomaterials that dissolve in aqueous fluids. Zinc oxide nanomaterials are of particular concern because dissolution leads to release of the toxic divalent zinc ion. Although zinc ions have been implicated in ZnO cytotoxicity, direct identification of the chemical form of zinc taken up by cells exposed to ZnO nanoparticles, and its intracellular fate, has not yet been achieved. We combined high resolution X-ray spectromicroscopy and high elemental sensitivity X-ray microprobe analyses to determine the fate of ZnO and less soluble iron-doped ZnO nanoparticles following exposure to cultures of human bronchial epithelial cells, BEAS-2B. We complemented two-dimensional X-ray imaging methods with atomic force microscopy of cell surfaces to distinguish between nanoparticles that were transported inside the cells from those that adhered to the cell exterior. The data suggest cellular uptake of ZnO nanoparticles is a mechanism of zinc accumulation in cells. Following uptake, ZnO nanoparticles dissolved completely generating intracellular Zn(2+) complexed by molecular ligands. These results corroborate a model for ZnO nanoparticle toxicity that is based on nanoparticle uptake followed by intracellular dissolution.

Selenium-Tolerant Diamondback Moth Disarms Hyperaccumulator Plant Defense

BACKGROUND Some plants hyperaccumulate the toxic element selenium (Se) to extreme levels, up to 1% of dry weight. The function of this intriguing phenomenon is obscure. RESULTS Here, we show that the Se in the hyperaccumulator princes plume (Stanleya pinnata) protects it from caterpillar herbivory because of deterrence and toxicity. In its natural habitat, however, a newly discovered variety of the invasive diamondback moth (Plutella xylostella) has disarmed this elemental defense. It thrives on plants containing highly toxic Se levels and shows no oviposition or feeding deterrence, in contrast to related varieties. Interestingly, a Se-tolerant wasp (Diadegma insulare) was found to parasitize the tolerant moth. The insects Se tolerance mechanism was revealed by X-ray absorption spectroscopy and liquid chromatography-mass spectroscopy, which showed that the Se-tolerant moth and its parasite both accumulate methylselenocysteine, the same form found in the hyperaccumulator plant, whereas related sensitive moths accumulate selenocysteine. The latter is toxic because of its nonspecific incorporation into proteins. Indeed, the Se-tolerant diamondback moth incorporated less Se into protein. Additionally, the tolerant variety sequestered Se in distinct abdominal areas, potentially involved in detoxification and larval defense to predators. CONCLUSIONS Although Se hyperaccumulation protects plants from herbivory by some invertebrates, it can give rise to the evolution of unique Se-tolerant herbivores and thus provide a portal for Se into the local ecosystem. In a broader context, this study provides insight into the possible ecological implications of using Se-enriched crops as a source of anti-carcinogenic selenocompounds and for the remediation of Se-polluted environments.

Spatially Resolved Characterization of Biogenic Manganese Oxide Production within a Bacterial Biofilm

ABSTRACT Pseudomonas putida strain MnB1, a biofilm-forming bacterial culture, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of aqueous Mn+2 [Mn+2(aq)] by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm, using scanning transmission X-ray microscopy (STXM) combined with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at the Mn L2,3 absorption edges. Subsamples were collected from growth flasks containing 0.1 and 1 mM total Mn at 16, 24, 36, and 48 h after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at a 40-nm resolution. Manganese NEXAFS spectra were extracted from X-ray energy sequences of STXM images (stacks) and fit with linear combinations of well-characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III), and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn+2(aq) was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission X-ray microscopy is a promising tool for advancing the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.

Asymmetric catalysis at the mesoscale: gold nanoclusters embedded in chiral self-assembled monolayer as heterogeneous catalyst for asymmetric reactions.

Research to develop highly versatile, chiral, heterogeneous catalysts for asymmetric organic transformations, without quenching the catalytic reactivity, has met with limited success. While chiral supramolecular structures, connected by weak bonds, are highly active for homogeneous asymmetric catalysis, their application in heterogeneous catalysis is rare. In this work, asymmetric catalyst was prepared by encapsulating metallic nanoclusters in chiral self-assembled monolayer (SAM), immobilized on mesoporous SiO2 support. Using olefin cyclopropanation as an example, it was demonstrated that by controlling the SAM properties, asymmetric reactions can be catalyzed by Au clusters embedded in chiral SAM. Up to 50% enantioselectivity with high diastereoselectivity were obtained while employing Au nanoclusters coated with SAM peptides as heterogeneous catalyst for the formation of cyclopropane-containing products. Spectroscopic measurements correlated the improved enantioselectivity with the formation of a hydrogen-bonding network in the chiral SAM. These results demonstrate the synergetic effect of the catalytically active metallic sites and the surrounding chiral SAM for the formation of a mesoscale enantioselective catalyst.

Trichomes of Tobacco Excrete Zinc as Zinc-Substituted Calcium Carbonate and Other Zinc-Containing Compounds

Tobacco (Nicotiana tabacum L. cv Xanthi) plants were exposed to toxic levels of zinc (Zn). Zn exposure resulted in toxicity signs in plants, and these damages were partly reduced by a calcium (Ca) supplement. Confocal imaging of intracellular Zn using Zinquin showed that Zn was preferentially accumulated in trichomes. Exposure to Zn and Zn + Ca increased the trichome density and induced the production of Ca/Zn mineral grains on the head cells of trichomes. These grains were aggregates of submicrometer-sized crystals and poorly crystalline material and contained Ca as major element, along with subordinate amounts of Zn, manganese, potassium, chlorine, phosphorus, silicon, and magnesium. Micro x-ray diffraction revealed that the large majority of the grains were composed essentially of metal-substituted calcite (CaCO3). CaCO3 polymorphs (aragonite and vaterite) and CaC2O4 (Ca oxalate) mono- and dihydrate also were identified, either as an admixture to calcite or in separate grains. Some grains did not diffract, although they contained Ca, suggesting the presence of amorphous form of Ca. The presence of Zn-substituted calcite was confirmed by Zn K-edge micro-extended x-ray absorption fine structure spectroscopy. Zn bound to organic compounds and Zn-containing silica and phosphate were also identified by this technique. The proportion of Zn-substituted calcite relative to the other species increased with Ca exposure. The production of Zn-containing biogenic calcite and other Zn compounds through the trichomes is a novel mechanism involved in Zn detoxification. This study illustrates the potential of laterally resolved x-ray synchrotron radiation techniques to study biomineralization and metal homeostasis processes in plants.