Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models

Metabolomics studies generate increasingly complex data tables, which are hard to summarize and visualize without appropriate tools. The use of chemometrics tools, e.g., principal component analysis (PCA), partial least-squares to latent structures (PLS), and orthogonal PLS (OPLS), is therefore of great importance as these include efficient, validated, and robust methods for modeling information-rich chemical and biological data. Here the S-plot is proposed as a tool for visualization and interpretation of multivariate classification models, e.g., OPLS discriminate analysis, having two or more classes. The S-plot visualizes both the covariance and correlation between the metabolites and the modeled class designation. Thereby the S-plot helps identifying statistically significant and potentially biochemically significant metabolites, based both on contributions to the model and their reliability. An extension of the S-plot, the SUS-plot (shared and unique structure), is applied to compare the outcome of multiple classification models compared to a common reference, e.g., control. The used example is a gas chromatography coupled mass spectroscopy based metabolomics study in plant biology where two different transgenic poplar lines are compared to wild type. By using OPLS, an improved visualization and discrimination of interesting metabolites could be demonstrated.     

Interferometric null test of a deep parabolic reflector generating a Hertzian dipole field

We report on interferometric characterization of a deep parabolic mirror with a depth of more than five times its focal length. The interferometer is of Fizeau type; its core consists of the mirror itself, a spherical null element, and a reference flat. Because of the extreme solid angle produced by the paraboloid, the alignment of the setup appears to be very critical and needs auxiliary systems for control. Aberrations caused by misalignments are removed via fitting of suitable functionals provided by means of ray tracing simulations. It turns out that the usual misalignment approximations fail under these extreme conditions.     

In vitro accessibility of β‐carotene from cooked Sri Lankan green leafy vegetables and their estimated contribution to vitamin A requirement

Vitamin A deficiency is an important issue for public health in Sri Lanka, where pro‐vitamin A carotenoids from green leafy vegetables provide most of the dietary vitamin A. The objective of this study was to analyse the β‐carotene content of seven types of green leafy vegetables and calculate the contribution of one traditionally cooked portion to the recommended daily allowance (RDA) of retinol. The total amount and in vitro accessibility of β‐carotene were determined using HPLC. The in vitro method simulates the conditions in the human intestinal tract. The all‐trans‐β‐carotene content in the fresh blanched vegetables ranged from 149 µg g^?1 dry weight (DW) in leaves of Alternanthera sessilis (mukunuwanna) to 565 µg g^?1 DW in Amaranthus caudatus (thampala). One portion (100 g) of green leaves cooked without fat (coconut) only contributed from 140 to 180 µg mg^?1 of the recommended daily allowance. A. sessilis, Centella asiatica (gotukola), Spinacea oleracea (nivithi) and A. caudatus, cooked with coconut fat contributed 140–680 µg mg^?1. However, stir‐fried or ‘malluma’ preparations (with coconut products) of Sesbania grandiflora (kathurumurunga) and Manihot esculenta (manioc) may provide more than 1.59–4.37 times the RDA of retinol. These results show that not only the choice of green leaves used but also the addition of fat while cooking is of great importance. Copyright © 2005 Society of Chemical Industry     

Microstructure Evolution of Atomized Al-0.61 wt pct Fe and Al-1.90 wt pct Fe Alloys

The microstructure evolution of impulse atomized powders of Al-0.61 wt pct and Al-1.90 wt pct Fe compositions have been investigated with a scanning electron microscope, transmission electron microscope, neutron diffraction, and backscattering electron diffraction (EBSD). Both hypoeutectic and hypereutectic compositions demonstrated similar macrostructure (i.e., primary α-Al dendrites/cells with eutectic Al-Fe intermetallics decorated at the dendritic/cellular walls). Selected area electron diffraction (SAED) analysis and SAED pattern simulation identified the eutectic Al-Fe intermetallic as Al_mFe (m = 4.0-4.4). This is verified by neutron diffraction analysis. Cubic texture was observed by EBSD on the droplets with dendritic growth direction close to 〈111〉. The possible reasons are discussed.     

Cd-free buffer layers for CIGS solar cells prepared by a dry process

ZnSe buffer layers for Cu(ln,Ga)Se₂/buffer/ZnO solar cells have been prepared by metal organic chemical vapor deposition (MOCVD). Using photoassisted MOCVD, deposition temperatures down to 265°C are possible. It is shown that deposition temperatures well below 300°C are essential as well as deposition times not much longer than 3 min. Higher temperatures and longer deposition times lead to absorber degradation. With optimized buffer deposition efficiencies of 11% have been obtained on CIGS absorbers from the Siemens pilot production line.     

Bonding of ppb levels of methyl mercury to reduced sulfur groups in soil organic matter

The strong binding of CH3Hg+ to natural organic matter (NOM) in soils and waters determines the speciation of CH3Hg under aerobic conditions and indirectly its bioavailability and rates of demethylation. In lab experiments, halides (Cl, Br, I) were used as competing ligands to determine the strength of CH3Hg+ binding to solid-phase soil organic carbon (SOC) and to dissolved soil organic carbon (DOC) as a function of time, pH, and concentration of halide. Experiments were conducted with native concentrations of CH3Hg (1.7-9.8 ng g(-1)) in organic soils, and equilibrium concentrations of CH3Hg were determined by species-specific-isotope-dilution (SSID) gas-chromatography-induced-coupled-plasma-mass-spectrometry (GC-ICP-MS). A simple model (RS- + CH3Hg+ = CH3HgSR; log KCH3HgSR) was used to simulate the binding to SOC and DOC, in which the binding sites (RSH) were independently determined by X-ray absorption near-edge structure (XANES) spectroscopy. The pKa values of RSH groups were fixed at 8.50 and 9.95, reflecting the two major thiol groups in proteins. Log KCH3HgSR values determined for SOC and DOC were similar, showing a range of 15.6-17.1 for all experiments covering a pH range of 2.0-5.1. Despite large differences in affinities between Cl, Br, and I for CH3Hg+, determined constants were independent of type and concentration of halide used in the experiments (log KCH3HgSR = 16.1-16.7 at pH 3.5-3.6). Even if our log KCH3HgSR values were conditional in that they decreased with pH above 3.5, they were in fair agreement with stability constants determined for the association between CH3Hg+ and thiol groups in well-defined organic molecules (log K1 = 15.7-17.5). Speciation calculations based on our results show that, in absence of substantial concentrations of inorganic sulfides, neutral chloro-complexes (CH3HgCl) and free CH3Hg+ reach concentrations on the order of 10(-17)-10(-18) M at pH 5 in soil solutions with 3 x 10(-5) M of chloride.     

Inactivation of Escherichia coli, Listeria innocua and Saccharomyces cerevisiae in relation to membrane permeabilization and subsequent leakage of intracellular compounds due to pulsed electric field processing

Membrane permeabilization, caused by pulsed electric field (PEF) processing of microbial cells, was investigated by measurement of propidium iodide (PI) uptake with flow cytometry. Inactivation of Escherichia coli, Listeria innocua and Saccharomyces cerevisiae was determined by viable counts, and leakage of intracellular compounds, such as ATP and UV-absorbing substances, was measured in the extracellular environment. Electrical field strength and pulse duration influenced membrane permeabilization of all three tested organisms of which S. cerevisiae was the most PEF sensitive, followed by E. coli and L. innocua. It was shown by viable counts, PI uptake and leakage of intracellular compounds that L. innocua was the most resistant. Increased inactivation corresponded to greater numbers of permeabilized cells, which were reflected by increased PI uptake and larger amounts of intracellular compounds leaking from cells. For E. coli and L. innocua, a linear relationship was observed between the number of inactivated cells (determined as CFU) and cells with permeated membranes (determined by PI uptake), with higher number of inactivated cells than permeated cells. Increased leakage of intracellular compounds with increasing treatment severity provided further evidence that cells were permeabilized. For S. cerevisiae, there was higher PI uptake after PEF treatments, although very little or no inactivation was observed. Results suggest that E. coli and L. innocua cells, which took up PI, lost their ability to multiply, whereas cells of S. cerevisiae, which also took up PI, were not necessarily lethally permeabilized.