Chithra Karunakaran

Nanoscale Chemical Imaging of the Reduction Behavior of a Single Catalyst Particle

A closer look: Investigation of the reduction properties of a single Fischer-Tropsch catalyst particle, using in situ scanning transmission X-ray microscopy with spatial resolution of 35 nm, reveals a heterogeneous distribution of Fe(0), Fe(2+), and Fe(3+) species. Regions of different reduction properties are defined and explained on the basis of local chemical interactions and catalyst morphology.

Soft X-Ray Inspection of Wheat Kernels Infested by Sitophilus oryzae

The potential of a soft X–ray method (15 kV and 65 .A) to detect internal seed infestations by the rice weevil (Sitophilus oryzae) in Canada Western Red Spring wheat was determined in this study. The infested kernels were identified by the presence of egg plugs and were scanned with a real–time fluoroscope every 5 to 7 d until the adults emerged from the kernels. A total of 57 features using histogram groups, textural features, and histogram and shape moments were extracted from the X–ray images of the wheat kernels. Parametric and non–parametric classifiers, and a 4–layer back propagation neural network classifier were used to identify uninfested and infested wheat kernels using histogram and textural features independently, and using all 57 features together. There was no significant difference between the classifiers for the identification of uninfested and infested wheat kernels. More than 95% of uninfested kernels and kernels infested by larval stages were correctly identified by all the classifiers. Wheat kernels infested by pupae–adults and insect–damaged kernels were identified with more than 99% accuracy by the classifiers.

Soft X-ray Spectromicroscopy Study of Mineral-Organic Matter Associations in Pasture Soil Clay Fractions

There is a growing acceptance that associations with soil minerals may be the most important overarching stabilization mechanism for soil organic matter. However, direct investigation of organo-mineral associations has been hampered by a lack of methods that can simultaneously characterize organic matter (OM) and soil minerals. In this study, STXM-NEXAFS spectroscopy at the C 1s, Ca 2p, Fe 2p, Al 1s, and Si 1s edges was used to investigate C associations with Ca, Fe, Al, and Si species in soil clay fractions from an upland pasture hillslope. Bulk techniques including C and N NEXAFS, Fe K-edge EXAFS spectroscopy, and XRD were applied to provide additional information. Results demonstrated that C was associated with Ca, Fe, Al, and Si with no separate phase in soil clay particles. In soil clay particles, the pervasive C forms were aromatic C, carboxyl C, and polysaccharides with the relative abundance of carboxyl C and polysaccharides varying spatially at the submicrometer scale. Only limited regions in the soil clay particles had aliphatic C. Good C-Ca spatial correlations were found for soil clay particles with no CaCO3, suggesting a strong role of Ca in organo-mineral assemblage formation. Fe EXAFS showed that about 50% of the total Fe in soils was contained in Fe oxides, whereas Fe-bearing aluminosilicates (vermiculite and Illite) accounted for another 50%. Fe oxides in the soil were mainly crystalline goethite and hematite, with lesser amounts of poorly crystalline ferrihydrite. XRD revealed that soil clay aluminosilicates were hydroxy-interlayered vermiculite, Illite, and kaolinite. C showed similar correlation with Fe to Al and Si, implying a similar association of Fe oxides and aluminosilicates with organic matter in organo-mineral associations. These direct microscopic determinations can help improve understanding of organo-mineral interactions in soils.

ATR–FTIR spectroscopy reveals involvement of lipids and proteins of intact pea pollen grains to heat stress tolerance

With climate change, pea will be more frequently subjected to heat stress in semi-arid regions like Saskatchewan during flowering. The pollen germination percentage of two pea cultivars was reduced by heat stress (36°C) with an important decrease in cultivar ‘CDC Golden’ compared to ‘CDC Sage.’ Lipids, protein and other pollen coat compositions of whole intact pollen grains of both pea cultivars were investigated using mid infrared (mid-IR) attenuated total reflectance (ATR)–Fourier transform infrared (FTIR) spectroscopy. Curve fitting of ATR absorbance spectra in the protein region enabled estimation and comparison of different protein secondary structures between the two cultivars. CDC Sage had relatively greater amounts of α-helical structures (48.6–43.6%; band at 1654 cm-1) and smaller amounts of β-sheets (41.3–46%) than CDC Golden. The CDC Golden had higher amounts of β-sheets (46.3–51.7%) compared to α-helical structures (35.3–36.2%). Further, heat stress resulted in prominent changes in the symmetrical and asymmetrical CH2 bands from lipid acyl chain, ester carbonyl band, and carbohydrate region. The intensity of asymmetric and symmetric CH2 vibration of heat stressed CDC Golden was reduced considerably in comparison to the control and the decrease was higher compared to CDC Sage. In addition, CDC Golden showed an increase in intensity at the oxidative band of 3015 cm-1. These results reveal that the whole pollen grains of both pea cultivars responded differently to heat stress. The tolerance of CDC Sage to heat stress (expressed as pollen germination percentage) may be due to its protein richness with α-helical structures which would protect against the destructive effects of dehydration due to heat stress. The low pollen germination percentage of CDC Golden after heat stress may be also due to its sensitivity to lipid changes due to heat stress.

Microbial Architecture of Environmental Sulfur Processes: A Novel Syntrophic Sulfur-Metabolizing Consortia

Microbial oxidation of sulfur-rich mining waste materials drives acid mine drainage (AMD) and affects the global sulfur biogeochemical cycle. The generation of AMD is a complex, dynamic process that proceeds via multiple reaction pathways. The role of natural consortia of microbes in AMD generation, however, has received very little attention despite their widespread occurrence in mining environments. Through a combination of geochemical experimentation and modeling, scanning transmission X-ray microscopy, and fluorescent in situ hybridization, we show a novel interdependent metabolic arrangement of two ubiquitous and abundant AMD bacteria: chemoautotrophic sulfur-oxidizing Acidithiobacillus sp. and heterotrophic Acidiphilium sp. Highly reminiscent of anaerobic methane oxidation (AOM) consortia, these bacteria are spatially segregated within a planktonic macrostructure of extracellular polymeric substance in which they syntrophically couple sulfur oxidation and reduction reactions in a mutually beneficial arrangement that regenerates their respective sulfur substrates. As discussed here, the geochemical impacts of microbial metabolism are linked to the consortial organization and development of the pod structure, which affects cell-cell interactions and interactions with the surrounding geochemical microenvironment. If these pods are widespread in mine waters, echoing the now widespread discovery of AOM consortia, then AMD-driven CO(2) atmospheric fluxes from H(2)SO(4) carbonate weathering could be reduced by as much as 26 TgC/yr. This novel sulfur consortial discovery indicates that organized metabolically linked microbial partnerships are likely widespread and more significant in global elemental cycling than previously considered.

Seed set, pollen morphology and pollen surface composition response to heat stress in field pea

Pea (Pisum sativum L.) is a major legume crop grown in a semi-arid climate in Western Canada, where heat stress affects pollination, seed set and yield. Seed set and pod growth characteristics, along with in vitro percentage pollen germination, pollen tube growth and pollen surface composition, were measured in two pea cultivars (CDC Golden and CDC Sage) subjected to five maximum temperature regimes ranging from 24 to 36 °C. Heat stress reduced percentage pollen germination, pollen tube length, pod length, seed number per pod, and the seed-ovule ratio. Percentage pollen germination of CDC Sage was greater than CDC Golden at 36 °C. No visible morphological differences in pollen grains or the pollen surface were observed between the heat and control-treated pea. However, pollen wall (intine) thickness increased due to heat stress. Mid-infrared attenuated total reflectance (MIR-ATR) spectra revealed that the chemical composition (lipid, proteins and carbohydrates) of each cultivars pollen grains responded differently to heat stress. The lipid region of the pollen coat and exine of CDC Sage was more stable compared with CDC Golden at 36 °C. Secondary derivatives of ATR spectra indicated the presence of two lipid types, with different amounts present in pollen grains from each cultivar.

Chemical speciation of nanoparticles surrounding metal-on-metal hips

Spectromicroscopy of tissue surrounding failed CoCr metal-on-metal hip replacements detected corroded nanoscale debris in periprosthetic tissue in two chemical states, with concomitant mitochondrial damage. The majority of debris contained Cr(3+), with trace amounts of oxidised cobalt. A minority phase containing a core of metallic chromium and cobalt was also observed.

Methylmercury targets photoreceptor outer segments.

Human populations experience widespread low level exposure to organometallic methylmercury compounds through consumption of fish and other seafood. At higher levels, methylmercury compounds specifically target nervous systems, and among the many effects of their exposure are visual disturbances, including blindness, which previously were thought to be due to methylmercury-induced damage to the visual cortex. Here, we employ high-resolution X-ray fluorescence imaging using beam sizes of 500 × 500 and 250 × 250 nm(2) to investigate the localization of mercury at unprecedented resolution in sections of zebrafish larvae ( Danio rerio ), a model developing vertebrate. We demonstrate that methylmercury specifically targets the outer segments of photoreceptor cells in both the retina and pineal gland. Methylmercury distribution in both tissues was correlated with that of sulfur, which, together with methylmercurys affinity for thiolate donors, suggests involvement of protein cysteine residues in methylmercury binding. In contrast, in the lens, the mercury distribution was different from that of sulfur, with methylmercury specifically accumulating in the secondary fiber cells immediately underlying the lens epithelial cells rather than in the lens epithelial cells themselves. Since methylmercury targets two main eye tissues (lens and photoreceptors) that are directly involved in visual perception, it now seems likely that the visual disruption associated with methylmercury exposure in higher animals including humans may arise from direct damage to photoreceptors, in addition to injury of the visual cortex.

Synchrotron Radiation Sheds Fresh Light on Plant Research: The Use of Powerful Techniques to Probe Structure and Composition of Plants

While synchrotron radiation is a powerful tool in material and biomedical sciences, it is still underutilized in plant research. This mini review attempts to introduce the potential of synchrotron-based spectroscopic and imaging methods and their applications to plant sciences. Synchrotron-based Fourier transform infrared spectroscopy, X-ray absorption and fluorescence techniques, and two- and three-dimensional imaging techniques are examined. We also discuss the limitations of synchrotron-based research in plant sciences, specifically the types of plant samples that can be used. Despite limitations, the unique features of synchrotron radiation such as high brightness, polarization and pulse properties offer great advantages over conventional spectroscopic and imaging tools and enable the correlation of the structure and chemical composition of plants with biochemical function. Modern detector technologies and experimental methodologies are thus enabling plant scientists to investigate aspects of plant sciences such as ultrafast kinetics of biochemical reactions, mineral uptake, transport and accumulation, and dynamics of cell wall structure and composition during environmental stress in unprecedented ways using synchrotron beamlines. The potential for the automation of some of these synchrotron technologies and their application to plant phenotyping is also discussed.

Accurate dosimetry in scanning transmission X‐ray microscopes via the cross‐linking threshold dose of poly(methyl methacrylate)

The sensitivity of various polymers to radiation damage by soft X-rays has been measured previously with scanning transmission X-ray microscopes. However, the critical dose values reported by different groups for the same material differ by more than 100%. Possible sources of this variability are investigated here for poly(methyl methacrylate) (PMMA) using controlled exposure to monochromatic soft X-rays at 300 eV. Radiation sensitivity, judged by several different criteria, was evaluated as a function of dose rate, pre-exposure thermal treatments and X-ray polarization. Both the measured critical dose and the dose required to initiate negative mode (cross-linking) were observed to depend only on dose, not the other factors explored. A method of determining detector efficiency from the dose required to initiate negative mode in PMMA is outlined. This method was applied to many of the soft X-ray STXMs presently operating to derive the efficiencies of their transmitted X-ray detectors in the C 1s absorption-edge region.