Synchrotron-based Scanning Transmission X-ray Microscopy Research Articles

The cytotoxicity of cadmium-based quantum dots

Semiconductor Quantum dots (QDs) have raised great attention because of their superior optical properties and wide utilization in biological and biomedical studies. More recently, there have been intense concerns on cytotoxicity assessment of QDs. Most QDs are made of heavy metal ions (e.g., Cd2+), which may result in potential in vitro toxicity that hampers their practical applications. In this article, we aim to summarize recent progress on mechanistic studies of cytotoxicity of II–IV QDs. We have studied the cytotoxicity of a series of aqueous synthesized QDs (aqQDs), i.e. CdTe, CdTe/CdS core-shell structured and CdTe/CdS/ZnS core-shell-shell structured aqQDs. Our results suggested that released cadmium ions are responsible for the observed cytotoxicity of cadmium-based QDs. The fact that CdTe/CdS/ZnS core-shell-shell structured QDs are nearly nontoxic to cells further confirmed the role of released cadmium ions on cytotoxicity, and the effective protection of the ZnS shell. However, intracellular level of Cd2+ ions cannot be the only reason since the comparison with CdCl2-treated cells suggests there are other factors contributed to the cytotoxicity of aqQDs. Our studies on genome-wide gene expression profiling and subcellular localization of aqQDs with synchrotron-based scanning transmission X-ray microscopy (STXM) further suggest that the cytotoxicity of CdTe QDs not only comes from the release of Cd2+ ions but also intracellular distribution of QD nanoparticles in cells and the associated nanoscale effects.

Preservation of protein globules and peptidoglycan in the mineralized cell wall of nitrate-reducing, iron(II)-oxidizing bacteria: a cryo-electron microscopy study

Iron-oxidizing bacteria are important actors of the geochemical cycle of iron in modern environments and may have played a key role all over Earth's history. However, in order to better assess that role on the modern and the past Earth, there is a need for better understanding the mechanisms of bacterial iron oxidation and for defining potential biosignatures to be looked for in the geologic record. In this study, we investigated experimentally and at the nanometre scale the mineralization of iron-oxidizing bacteria with a combination of synchrotron-based scanning transmission X-ray microscopy (STXM), scanning transmission electron microscopy (STEM) and cryo-transmission electron microscopy (cryo-TEM). We show that the use of cryo-TEM instead of conventional microscopy provides detailed information of the successive iron biomineralization stages in anaerobic nitrate-reducing iron-oxidizing bacteria. These results suggest the existence of preferential Fe-binding and Fe-oxidizing sites on the outer face of the plasma membrane leading to the nucleation and growth of Fe minerals within the periplasm of these cells that eventually become completely encrusted. In contrast, the septa of dividing cells remain nonmineralized. In addition, the use of cryo-TEM offers a detailed view of the exceptional preservation of protein globules and the peptidoglycan within the Fe-mineralized cell walls of these bacteria. These organic molecules and ultrastructural details might be protected from further degradation by entrapment in the mineral matrix down to the nanometre scale. This is discussed in the light of previous studies on the properties of Fe-organic interactions and more generally on the fossilization of mineral-organic assemblies.

Geochemical evolution of organic-rich shales with increasing maturity: A STXM and TEM study of the Posidonia Shale (Lower Toarcian, northern Germany)

Hydrocarbon generation and retention processes occurring within gas shales as a response to increases in thermal maturation are still poorly constrained. While efforts have been directed at unravelling the resource potential, composition and textures of these economically important unconventional systems, their spatial variability in chemistry and structure is still poorly documented at the sub-micrometer scale. Here, we have characterized samples of the Lower Toarcian Posidonia Shale samples from northern Germany at varying stages of thermal maturation using a combination of compositional organic geochemistry and spectromicroscopy techniques, including synchrotron-based scanning transmission X-ray microscopy (STXM). We document geochemical and mineralogical heterogeneities down to the nanometer scale within the investigated samples as a function of their level of thermal maturity. In particular, authigenic albite crystals containing nanometric halite inclusions have been documented within the investigated mature and overmature samples. The presence of such tracers of palaeobrine–carbonate interactions supports a maturation scenario for the Lower Toarcian Posidonia Shale intimately related to ascending brine fluids rather than a maturation scenario solely resulting from high heat flows. In addition, various types of asphaltene- and NSO-rich bitumen have been detected within the same samples, very likely genetically derived from thermally degraded organic precursors. Furthermore, the formation of nanoporous pyrobitumen has been inferred for samples of gas window maturity, likely resulting from the formation of gaseous hydrocarbons. By providing in-situ insights into the fate of bitumen and pyrobitumen as a response to the thermal evolution of the macromolecular structure of kerogen, the results reported here constitute an important step towards better constraining hydrocarbon generation processes during natural shale gas maturation.

Study of the crystallographic architecture of corals at the nanoscale by scanning transmission X-ray microscopy and transmission electron microscopy

We have investigated the nanotexture and crystallographic orientation of aragonite in a coral skeleton using synchrotron-based scanning transmission X-ray microscopy (STXM) and transmission electron microscopy (TEM). Polarization-dependent STXM imaging at 40-nm spatial resolution was used to obtain an orientation map of the c-axis of aragonite on a focused ion beam milled ultrathin section of a Porites coral. This imaging showed that one of the basic units of coral skeletons, referred to as the center of calcification (COC), consists of a cluster of 100-nm aragonite globules crystallographically aligned over several micrometers with a fan-like distribution and with the properties of single crystals at the mesoscale. The remainder of the skeleton consists of aragonite single-crystal fibers in crystallographic continuity with the nanoglobules comprising the COC. Our observation provides information on the nm-scale processes that led to biomineral formation in this sample. Importantly, the present study illustrates how the methodology described here, which combines HRTEM and polarization-dependent synchrotron-based STXM imaging, offers an interesting new approach for investigating biomineralizing systems at the nm-scale.

Graphene-templated formation of two-dimensional lepidocrocite nanostructures for high-efficiency catalytic degradation of phenols

Graphene is a two-dimensional nanomaterial with exceptionally interesting physical and chemical properties, which has been actively explored in nanoelectronics, nanodevices and nanoscale catalysis. Here we report a graphene-templated route toward mild, solution-phase synthesis of ultrathin single crystal lepidocrocite (γ-FeOOH) nanosheets with high aspect ratio. We find that when reduced graphene oxide (rGO) was incubated with FeCl3 of 20 wt% at 80 °C and in the presence of reducing reagents (e.g.hydrazine hydrate), close-spaced 2D nanosheets of γ-FeOOH was formed on the surface of rGO, with the average thickness of 2.1 nm. This ultrathin nanomaterial was characterized via a range of complementary techniques, transmission electron microscopy (TEM), high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), Mössbauer spectroscopy and synchrotron-based scanning transmission X-ray microscopy (STXM), which confirmed the formation of γ-FeOOH 2D nanosheets. Importantly, we explore the application of this novel nanomaterial as an efficient and stable catalyst for phenol treatment in wastewater.

Ancient graphite in the Eoarchean quartz–pyroxene rocks from Akilia in southern West Greenland I: Petrographic and spectroscopic characterization

Because all known Eoarchean (>3.65 Ga) volcano-sedimentary terranes are locked in granitoid gneiss complexes that have experienced high degrees of metamorphism and deformation, the origin and mode of preservation of carbonaceous material in the oldest metasedimentary rocks remain a subject of vigorous debate. To determine the biogenicity of carbon in graphite in such rocks, carbonaceous material must be demonstrably indigenous and its composition should be consistent with thermally altered biogenic carbon as well as inconsistent with abiogenic carbon. Here we report the petrological and spectroscopic characteristics of carbonaceous material, typically associated with individual apatite grains, but also with various other minerals including calcite, in a >3.83 Ga granulite-facies ferruginous quartz-pyroxene unit (Qp rock) from the island of Akilia in southern West Greenland. In thin sections of the fine-grained parts of Akilia Qp rock sample G91-26, mapped apatites were found to be associated with graphite in about 20% of the occurrences. Raman spectra of this carbonaceous material had strong G-band and small D-band absorptions indicative of crystalline graphite. Three apatite-associated graphites were found to contain curled graphite structures, identified by an anomalously intense second-order D-band (or 2D-band) Raman mode. These structures are similar to graphite whiskers or cones documented to form at high temperatures. Raman spectra of apatite-associated graphite were consistent with formation at temperatures calculated to be between 635 and 830 °C, which are consistent with granulite-facies metamorphic conditions. Three graphite targets extracted by focused ion beam (FIB) methods contained thin graphite coatings on apatite grains rather than inclusions sensu stricto as inferred from transmitted light microscopy and Raman spectroscopy. TEM analyses of graphite in these FIB sections showed a (0 0 0 2) interplanar spacing between 3.41 and 3.64 Å for apatite-associated graphite, which is larger than the spacing of pure graphite (3.35 Å) and may be caused by the presence of non-carbon heteroatoms in interlayer sites. Samples analyzed by synchrotron-based scanning transmission X-ray microscopy (STXM) also confirmed the presence of crystalline graphite, but abundances of N and O heteroatoms were below detection limit for this method. Graphite in the Akilia Qp rock was also found to occur in complex polyphase mineral assemblages of hornblende ± calcite ± sulfides ± magnetite that point to high-temperature precipitation from carbon-bearing fluids. These complex mineral assemblages may represent another generation of graphitization that could have occurred during the amphibolite-facies metamorphic event at 2.7 Ga. Several observations point to graphitization from high-temperature fluid-deposition for some of the Akilia graphite and our results do not exclude a biogenic source of carbon in graphite associated with apatite, but ambiguities remain for the origin of this carbon.

Humic acid metal cation interaction studied by spectromicroscopy techniques in combination with quantum chemical calculations

Humic acids (HA) have a high binding capacity towards traces of toxic metal cations, thus affecting their transport in aquatic systems. Eu(III)-HA aggregates are studied by synchrotron-based scanning transmission X-ray microscopy (STXM) at the carbon K-edge and laser scanning luminescence microscopy (LSLM) at the (5)D(0) --> (7)F(1,2) fluorescence emission lines. Both methods provide the necessary spatial resolution in the sub-micrometre range to resolve characteristic aggregate morphologies: optically dense zones embedded in a matrix of less dense material in STXM images correspond to areas with increased Eu(III) luminescence yield in the LSLM micrographs. In the C 1s-NEXAFS of metal-loaded polyacrylic acid (PAA), used as a HA model compound, a distinct complexation effect is identified. This effect is similar to trends observed in the dense fraction of HA/metal cation aggregates. The strongest complexation effect is observed for the Zr(IV)-HA/PAA system. This effect is confirmed by quantum chemical calculations performed at the ab initio level for model complexes with different metal centres and complex geometries. Without the high spatial resolution of STXM and LSLM and without the combination of molecular modelling with experimental results, the different zones indicating a ;pseudo'-phase separation into strong complexing domains and weaker complexing domains of HA would never have been identified. This type of strategy can be used to study metal interaction with other organic material.

Microprobe analysis of neutron irradiated and autoclaved zirconium niobium claddings using synchrotron-based hard X-ray imaging and spectroscopy

Two zirconium alloys (Zr–2.5%Nb) – one oxidized in a pressurized water reactor, the other oxidized in autoclave and used as reference – are analyzed by combining synchrotron-based scanning transmission and fluorescence X-ray microscopy and micro-X-ray absorption spectroscopy (micro-XAS). Two-dimensional zirconium distribution maps recorded on the neutron irradiated and the non-irradiated autoclaved Zr–2.5%Nb alloys clearly allow the localization of the oxide and the metal parts of the interface with a micrometer spatial resolution. Micro-XAS investigations make possible the determination of the speciation of zirconium and niobium both in the oxide and the metal parts of the interface for the irradiated and non-irradiated samples. The coordination environment and/or the valency of zirconium and niobium in the metal and the oxide parts of the interface have been determined for both materials, and interpreted on the basis of comparison with metal and oxide reference compounds.

Nanoscale Biogeocomplexity of the Organomineral Assemblage in Soil

Methodological constraints limit the extent to which existing soil aggregation models explain carbon (C) stabilization in soil. We hypothesize that the physical infrastructure of microaggregates plays a major role in determining the chemistry of the occluded C and intimate associations between particulate C, chemically stabilized C and the soil mineral matrix. We employed synchrotron‐based scanning transmission X‐ray microscopy (STXM) coupled with near‐edge X‐ray absorption fine structure (C 1s‐NEXAFS) spectroscopy to investigate the nanoscale physical assemblage and C chemistry of 150‐μm microaggregates from a Kenyan Oxisol. Ultra‐thin sections were obtained after embedding microaggregates in a sulfur block and sectioning on a cryo‐microtome at −55°C. Principal component and cluster analyses revealed four spatially distinct features: pore surfaces, mineral matter, organic matter, and their mixtures. The occurrence of these features did not vary between exterior and interior locations; however, the degree of oxidation decreased while the complexity and occurrence of aliphatic C forms increased from exterior to interior regions of the microaggregate. At both locations, compositional mapping rendered a nanoscale distribution of oxidized C clogging pores and coating pore cavities on mineral surface. Hydrophobic organic matter of aromatic and aliphatic nature, representing particulate C forms appeared physically occluded in 2‐ to 5‐μm pore spaces. Our findings demonstrate that organic matter in microaggregates may be found as either oxidized C associated with mineral surfaces or aromatic and aliphatic C in particulate form. Using STXM and C 1s‐NEXAFS we are for the first time able to resolve the nanoscale biogeocomplexity of unaltered soil microaggregates.