Information visualization techniques for sensing and biosensing

The development of new methods and concepts to visualize massive amounts of data holds the promise to revolutionize the way scientific results are analyzed, especially when tasks such as classification and clustering are involved, as in the case of sensing and biosensing. In this paper we employ a suite of software tools, referred to as PEx-Sensors, through which projection techniques are used to analyze electrical impedance spectroscopy data in electronic tongues and related sensors. The possibility of treating high dimension datasets with PEx-Sensors is advantageous because the whole impedance vs. frequency curves obtained with various sensing units and for a variety of samples can be analyzed at once. It will be shown that non-linear projection techniques such as Sammon's Mapping or IDMAP provide higher distinction ability than linear methods for sensor arrays containing units capable of molecular recognition, apparently because these techniques are able to capture the cooperative response owing to specific interactions between the sensing unit material and the analyte. In addition to allowing for a higher sensitivity and selectivity, the use of PEx-Sensors permits the identification of the major contributors for the distinguishing ability of sensing units and of the optimized frequency range. The latter will be illustrated with sensing units made with layer-by-layer (LbL) films to detect phytic acid, whose capacitance data were visualized with Parallel Coordinates. Significantly, the implementation of PEx-Sensors was conceived so as to handle any type of sensor based on any type of principle of detection, representing therefore a generic platform for treating large amounts of data for sensors and biosensors.     

Rapid determination of fumagillin residues in honey by liquid chromatography-tandem mass spectrometry using the QuEChERS method

A new, rapid, and efficient method for determining the fumagillin residues in honey was developed. The samples extracted were analyzed using LC/MS/MS. Chromatographic separation of fumagillin was performed in gradient mode on a C8 column (100 x 2.0 mm, 5 microm) at 40 degrees C. The mobile phase consisted of a mixture of 2 mM ammonium formate-0.01% formic acid solution and methanol; the flow rate was set to 0.2 mL/min. Under these conditions, it was possible to measure fumagillin and its isomers as a single peak. The sample preparation procedure used is based on the QuEChERS (quick, easy, cheap, effective, rugged, and safe) method, which is fast (approximately 30 min) and uses less organic solvent. The fumagillin was extracted with acetonitrile containing 0.1% formic acid, then purified using a solid-phase extraction method with an Oasis mixed-mode weak anion-exchange cartridge. The overall recovery of fumagillin ranged from 88.1 to 99.4%; the intra- and interassay CVs were <4.5% and <4.9%, respectively. The LOQ was 0.1 microg/kg. LC/MS/MS coupled with the QuEChERS method showed strong potential as a method for determining fumagillin residues in honey.     

Rational development of caged-biotin protein-labeling agents and some applications in live cells

Biotin-(strept)avidin complex is widely used in biotechnology because of its extremely high binding constant, but there is no report describing spatiotemporally controlled formation of the complex in live cells. Here, based on X-ray crystal structure analysis and calorimetric data, we designed and synthesized photoreleasable biotins, which show greatly reduced affinity for (strept)avidin, but recover native affinity after UV irradiation. For application at the cell surface, we introduced an amine-reactive moiety into these "caged" biotin molecules. Specific fluorescence imaging of live cells that had been labeled with these agents and then UV-irradiated, was accomplished by addition of streptavidin conjugated with a fluorophore. We also demonstrated the applicability of these compounds for UV-irradiated-cell-specific drug delivery by using caged-biotin-labeled cells, a prodrug, and streptavidin conjugated with a prodrug-activating enzyme.     

Using multidimensional projection techniques for reaching a high distinguishing ability in biosensing

Recent advances in the control of molecular engineering architectures have allowed unprecedented ability of molecular recognition in biosensing, with a promising impact for clinical diagnosis and environment control. The availability of large amounts of data from electrical, optical, or electrochemical measurements requires, however, sophisticated data treatment in order to optimize sensing performance. In this study, we show how an information visualization system based on projections, referred to as Projection Explorer (PEx), can be used to achieve high performance for biosensors made with nanostructured films containing immobilized antigens. As a proof of concept, various visualizations were obtained with impedance spectroscopy data from an array of sensors whose electrical response could be specific toward a given antibody (analyte) owing to molecular recognition processes. In addition to discussing the distinct methods for projection and normalization of the data, we demonstrate that an excellent distinction can be made between real samples tested positive for Chagas disease and Leishmaniasis, which could not be achieved with conventional statistical methods. Such high performance probably arose from the possibility of treating the data in the whole frequency range. Through a systematic analysis, it was inferred that Sammon's mapping with standardization to normalize the data gives the best results, where distinction could be made of blood serum samples containing 10(-7) mg/mL of the antibody. The method inherent in PEx and the procedures for analyzing the impedance data are entirely generic and can be extended to optimize any type of sensor or biosensor.     

A hydrogenase model system based on the sequence of cytochrome c: photochemical hydrogen evolution in aqueous media

The diiron carbonyl cluster is held by a native CXXC motif, which includes Cys14 and Cys17, in the cytochrome c sequence. It is found that the diiron carbonyl complex works well as a catalyst for H(2) evolution. It has a TON of ～80 over 2 h at pH 4.7 in the presence of a Ru-photosensitizer and ascorbate as a sacrificial reagent in aqueous media.     

Ellagic Acid Suppresses ApoB Secretion and Enhances ApoA-1 Secretion from Human Hepatoma Cells,HepG2

The effect of ellagic acid (EA), a naturally occurring polyphenolic compound, on the secretion of apolipoproteins from human hepatocytes, HepG2, was investigated. The levels of apoB and apoA-1 secreted in the cell culture medium were determined by sandwich ELISA. EA did not affect cell viability at the tested concentrations (up to 50 µM). EA suppressed the secretion of apoB and enhanced that of apoA-1 from HepG2 cells. However, cellular apoB levels were increased, suggesting that EA inhibited the trafficking of apoB during the process of secretion. In contrast, the increase in the cellular levels of apoA-1 was consistent with its secreted levels. These results indicate that EA inhibits the secretion of apoB from hepatocytes and increases the secretion of apoA-1. Both of these effects are beneficial for lipoprotein metabolism in the prevention of lifestyle-related diseases. The detailed mechanism underlying these effects of EA on lipoprotein metabolism should be elucidated in the future, but this naturally occurring polyphenolic compound might be antihyperlipidemic. Based on these results, EA is suggested as a candidate food-derived compound for the prevention of hyperlipidemia.     

Kinetics of phase transformation from hBN to cBN in the presence of Mg3BN3 catalyst

Abstract

Transformation kinetics from hBN to cBN has been studied at 6 GPa with changing reaction temperature and content of catalyst mixed with hBN powder. At lower catalyst content (3–10 wt %), rate of transformation was extraordinary rapid between 1300 and 1350 C. At higher catalyst content (30–50 wt %), rate of transformation was decreased. Normal nucleation kinetics was observed at about 1500 C. The rapid transformation temperature region correlates characteristic behavior of the sintering process.     

Triplet state sublevel spectroscopy applied to proteins

Triplet state sublevel spectroscopy using optical detection of magnetic resonance (ODMR) in zero magnetic field can be successfully employed to study (i) the environment of tryptophan (Trp) residues in a protein by observing the position and structure of phosphorescence spectra, zero field ODMR transitions and triplet state sublevel kinetics, (ii) the energy transfer among Trp residues, and (iii) whether any cysteine (Cys) residue is within van der Waals distance of any Trp residue by studying the complex of the protein with methylmercury(II) iodide (CH₃HgI) which binds to Cys residues. These studies are particularly important where crystal structure study is not possible. Study of the S₁ state often gives ambiguous results since fluorescence is always broad and shows multi-exponential decay. Our results on bacteriophage lysozyme T4 which contains three Trp residues at positions 126, 138 and 158 are presented. Measurements were facilitated by the use of a mutated enzyme containing one or two Trp-Tyr substitutions. The results indicate that (i) Trp 126 and 158 are solvent exposed, whereas Trp 138 is buried in a hydrophobic environment, (ii)S ↔S non-radiative energy transfer takes place predominantly from Trp 126 to Trp 158, and (iii) only Trp-158 undergoes a heavy atom perturbation, which affects selectively the z-sublevel (z is an out-of-plane axis of the indole plane) as a result of CH₃HgI binding to nearby Cys 97. We suggest that the Hg atom is located on the z-axis of Trp 158 in the complex. This interpretation is based on our investigations on the effect of orientation of heavy atom perturbers in some naphthalene-crown ether metal ion complexes.