An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis

An improved pixel-based approach for analyzing 2-DE images is presented. The key feature of the method is to create a mask based on all gels in the experiment using image morphology, followed by multivariate analysis on the pixel level. The method reduces the impact of noise and background by identifying regions in the image where protein spots are present, but make no assumption on individual spot boundaries for isolated spots. This makes it possible to detect significant changes in complex regions, and visualize these changes over multiple gels in an easy way. False missing values and spot volumes caused by imposing erroneous spot boundaries are thus circumvented. The approach presented gives improved pixel-based information from the gels, and is also an alternative to existing methods for data-reduction, significance testing and visualization of 2-DE data. Results are compared with software using a common spot boundary approach on an experiment consisting of 35 full size gel images. Gel alignment is required before analysis.     

Study on the long life radicals of hexanediol diacrylate in irradiated urea canal complexes in relation to post-polymerization by irradiation

The properties of radicals formed on irradiating long chain monomers in urea canal complexes were studied by ESR and related to the results of post-polymerzation. The initiating radicals (CH₃-?HCOOR) were trapped in canal complexes as a result of γ-irradiation at relatively high temperature such as 25° and the radicals converted to propagating radicals (～CH₂-?HOOR0 on heating to 70°. The temperature dependence of radical concentration was followed and the decay curves corresponded well with the results of post-polymerization.     

On the fundamental conjecture of HDMR: a Fourier analysis approach

Although the HDMR decomposition has become an important tool for the understanding of high dimensional functions, the fundamental conjecture underlying its practical utility is still open for theoretical analysis. In this paper, we introduce the HDMR decomposition in conjunction with the Fourier-HDMR approximation leading to the following conclusions: (1) we suggest a type of Fourier-HDMR approximation for certain classes of differentiable functions; (2) utilizing the Fourier-HDMR method, we prove the fundamental conjecture about the dominance of low order terms in the HDMR expansion under relevant conditions, and we also obtain error estimates of the truncated HDMR expansion up to order u; (3) we prove the domain decomposition approximation theorem which shows that the global Fourier-HDMR approximation is not always optimal for a given accuracy order; (4) and finally, a piecewise Fourier-HDMR approach is discussed for high dimensional modeling. These results help to further understand how to efficiently represent the high dimensional functions.     

On some interfacial fundamental characteristics for a general model of giant magnetoresistance

We present an analytical model for introducing interface roughness into giant magnetoresistance. The roughness acts mainly on the spin currents via the mixing relaxation time, in such a way, that the theoretical results suggest a direct experimental procedure.     

Rapid impedance method for predicting the potential shelf life of packaged pasteurized milk

The potential shelf life of packaged pasteurized milk was studied using a rapid impedance method. The results showed a high correlation between the shelf life of Fengxing and Xiang Man-lou pasteurized milks and between the detection time and the logarithm of colony-forming units per milliliter. The impedance detection time was measured after preliminary incubation at 30 degrees C for 6 h for 100 and 200 microL milk samples, or at 37 degrees C for 6 h for 100-400 microL milk samples for Fengxing pasteurized milk, and after 6 h preliminary incubation at 30 degrees C for 300 and 400 microL milk samples or 6 h at 37 degrees C for 100-400 microL milk samples for Xiang Man-lou pasteurized milk. Regressive equations were then constructed to predict the potential shelf life. Compared with the traditional method, the impedance method plus pre-incubation of milk at elevated temperatures (30 and 37 degrees C) was rapid, accurate, and convenient. The entire estimation process was completed within 11-14 and 14-20 h for Fengxing and Xiang Man-lou pasteurized milks, respectively.     

Validated HPAEC-PAD method for prebiotics determination in synbiotic fermented milks during shelf life

Interest concerning functional food has been growing in recent years, and much attention has been focused on the choice of prebiotic fibers and probiotic microorganisms added to food products with the aim of improving health, producing synbiotic products. In the work reported here, an innovative analytical method performed by high-performance anion-exchange chromatography (HPAEC) with pulsed electrochemical detection has been optimized and validated for application to the study of prebiotic effects in synbiotic fermented milk prepared by addition of probiotics. The proposed method permits the evaluation of fructooligosaccharides and inulooligosaccharides with degrees of polymerization of 6–7 and 4–7, respectively. Quantitative determination was performed on oligosaccharides, whose standards are not commercially available, by employing calibration curves built by adding a known amount of the fiber used as an ingredient to the matrix. The work provides results from a parallel study on simultaneous variations of prebiotics and probiotics during the shelf life of fermented milk samples. The main advantage over time-consuming, classic enzymatic methods, whose results are limited only to average fiber content, is the possibility of dosing each carbohydrate by performing a single HPAEC run. Validation in terms of detection and quantitation limits, linearity, precision, and recovery was carried out.     

An integrated quantum chemical and experimental approach for exploring the structures and properties of insensitive munitions interacting with ions in bulk water

Structural Chemistry - Alternatives to legacy munitions and explosives, materials that feature increased stability against external stimuli without compromising their energetic yields are currently...     

Effect of low-dose γ-irradiation on the shelf life and quality characteristics of minimally processed potato cubes under modified atmosphere packaging

The processing conditions involving γ-irradiation for minimally processed potato cubes were optimized by response surface methodology. The effect of γ-irradiation dose (0–1.5 kGy), citric acid concentration (0–1.0%), KMS concentration (0–1.0%) and their complex interaction on L, a, b value, hardness and total sugar content were studied using a central composite rotatable design of experiments. The results showed that at the optimum conditions (γ-irradiation dose 1.0 kGy; citric acid concentration 0.33% and KMS concentration 0.55%) the L-value was ⩾48.50%, a-value ⩽0.95, b-value ⩽7.5, hardness ⩾100 N, sucrose concentration ⩽0.19% and sensory score ⩾6.0 at the end of the storage period of 4 weeks.     

A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins

A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend the recently introduced idea of constrained geometric simulations of diffusive motions in proteins by biasing backbone motions of the protein, whereas side-chain motions are biased toward favorable rotamer states. The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. When applied to a data set of proteins with experimentally observed conformational changes, conformational variabilities are reproduced very well for 4 out of 5 proteins that show domain motions, with correlation coefficients r > 0.70 and as high as r = 0.92 in the case of adenylate kinase. In 7 out of 8 cases, NMSim simulations starting from unbound structures are able to sample conformations that are similar (root-mean-square deviation = 1.0-3.1 ?) to ligand bound conformations. An NMSim generated pathway of conformational change of adenylate kinase correctly describes the sequence of domain closing. The NMSim approach is a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or as starting points for more sophisticated sampling techniques.     

High resolution-separation of DNA bands by electrophoresis with a long gel in a fluorescence-detection DNA sequencer.

A high-resolution separation of DNA bands is achieved by electrophoresis with a long gel in DNA base sequencing using fluorescence detection. We separate 760 and 761 base DNA fragments using the 93 cm migration electrophoresis optimized for the separation of DNA bands. A T7 DNA polymerase and an Mn++ buffer are used in sequencing reactions to obtain fluorescence peaks of uniform strength, and the peak areas in the spectrum are used for recognizing the peak number in a cluster of successive peaks. This method is successfully applied to the DNA fragment spectrum obtained by 93 cm migration electrophoresis, which results in a single-band differentiation of bands of 1040 base DNA.     

An approach to the sensitivity of temperature-gradient gel electrophoresis in the detection of clonally expanded T-cells in cutaneous T-cell lymphoma

Detection of T-cell clonality by polymerase chain reaction (PCR) and high-resolution electrophoresis facilitates differentiation of early stages of cutaneous T-cell lymphoma (CTCL) from benign T-cell-rich dermatoses. However, data regarding the sensitivity of the various electrophoresis techniques differ remarkably. In the present study, the capacity of heteroduplex (HD)-loaded temperature-gradient gel electrophoresis (TGGE) to detect clonally expanded T-cells was assessed systematically and modifications to the procedure were defined. Using our standard protocol, HD-TGGE detected clonal T-cell receptor (TCR)-gamma PCR products, generated from the Jurkat cell line, down to a total of 2 ng/microL (14 ng) DNA. However, slowly migrating single strands of the clonal PCR product reduced the amount of the clonality indicating homoduplices. To overcome this single-strand formation, thus decreasing the detection limit, the urea concentration in the gel and the temperature ramp for the HD-formation were altered, as well as the temperature gradient in the gel. Application of the modified protocol resulted in a tenfold lower detection limit of 0.15 ng/microL (1.05 ng) DNA in the clonal band. The sensitivity of the adapted HD-TGGE was investigated by dilution experiments using the well established T-cell lines Jurkat, Molt-4, MyLa and SeAx. By these approaches clonal PCR products diluted in nonclonal PCR products were detectable down to concentrations of 5-10%. Comparably, in the case of mixtures of clonal in nonclonal DNA the detection limit reached 5-10% clonal DNA. However, by dilution of clonal cells in nonclonal peripheral blood mononuclear cells, which corresponds to in vivo conditions, a lower detection limit of approximately 1-5% was observed.     

An investigation of the feasibility of applying Raman microscopy for exploring stained glass

Raman microscopy (RM) is widely used in archaeometrical studies of pigments, geomaterials and biomaterials in the Cultural Heritage, but one domain has received relatively less attention: the colouring of stained glass. This feasibility study investigates the advantages and disadvantages of employing RM alone in this field by means of a study of modern commercial glasses, modern commercial pigments, and a few archaeological stained glasses, but especially by an experimental project whereby the authors created stained glass. The different kinds of possible unreacted or reacted material are rigorously established. The distinction between Na, K, Ca glasses was explored, as well as the red colouring of an industrial glass which was proved to be due to the presence of (Zn, Cd)S(x)Se(1-x). Yellow, green, blue and maroon pigments were studied before and after an initial firing and then after heating on glass. The quality of the Raman spectra varied enormously and was sometimes disappointing. Nevertheless RM successfully identified various coloured products such as bindheimite, crocoite, cobalt aluminate, haematite; relict reactants such as corundum, eskolaite and oxides of Co or Pb; and provided indications of other phases such as maghemite or Co-olivine. One conclusion is that the amount of chemical reaction between the pigments and the glass is small compared to the amount in between the pigments. Comments are made on the potential for dating archaeological glass from the known age of synthesis of the pigments, and of the dangers of this approach. Overall it has been shown that RM can be useful for studying stained glass, especially for remote in situ analytical operations with mobile RM, but one must expect some problems either with fluorescence or weak spectra.     

An optosensor for tryptophan with C18 silica gel as a substrate

 A flow-through optosensor for tryptophan with C18 silica gel as a substrate is proposed. It has been developed in conjunction with a flow-injection analysis system and is based on the retention of tryptophan on the C18 column and the enhancement of its fluorescence. The detection limit is 25 ng mL^-1 with a relative standard deviation of 2.9% for 7 determinations of 10 μg mL^-1 of tryptophan. Most of the common species do not interfere. The method has been successfully applied to a pharmaceutical preparation. Received: 8 July 1996/Revised: 26 September 1996/Accepted: 30 September 1996     

Investigation of two computerized procedures for energy-dispersive X-ray fluorescence spectrometry by the fundamental parameter approach

Both the computerized procedures investigated for x-ray fluorescence spectrometry exploit the fundamental parameter approach. Procedures 1 and 2 are without and with absolute calibration of the spectrometer, respectively. The basic fundamental parameter equations are shown and the equivalence with the notation of influence coefficients is demonstrated. The advantages and limitations of the two procedures are discussed. If the sample contains no appreciable fraction of light elements, procedure 1 is well suited for standardless quantitative calculations. Procedure 2 is not limited by this restriction, and its use may indicate if the qualitative elemental analysis is complete. Even in the case of incomplete qualitative analysis, procedure 2 gives usable quantitative results. Calibration inaccuracies with procedure 2 are easily tested by procedure 1, thus the two procedures complement each other.     

Transport properties of long straight nano-channels in electrolyte solutions: a systematic approach

The principle of local thermodynamic equilibrium is systematically employed for obtaining various transport properties of long straight nano-channels. The concept of virtual solution is used to describe situations of non-negligible overlap of diffuse parts of electric double layers (EDLs) in nano-channels. Generic expressions for a variety of transport properties of long straight nano-channels are obtained in terms of quasi-equilibrium distribution coefficients of ions and functionals of quasi-equilibrium distribution of electrostatic potential. Further, the Poisson-Boltzmann approach is used to specify these expressions for long straight slit-like nano-channels. In the approximation of non-overlapped diffuse parts of double electric layers in nano-channels, simple analytical expressions are obtained for the apparent electrophoretic mobilities of (trace) analytes of arbitrary charge as well as for the salt reflection coefficient (osmotic pressure), salt diffusion permeability and electro-viscosity (electrokinetic energy conversion). The approximate solutions are compared with the results of rigorous solution of non-linearized Poisson-Boltzmann equation, and the accuracy of approximation is shown to be typically excellent when the nano-channel half-height exceeds ca.3 Debye screening lengths. Due to non-negligible electrostatic adsorption of ions by nano-channels, the apparent electrophoretic mobilities of counter-ionic analytes in nano-channels are smaller than in micro-channels whereas those of co-ionic analytes are larger. This dependence on the charge is useful for the separation of analytes of close electrophoretic mobilities. The osmotic pressure is shown to be positive, negative or pass through maxima as a function of applied salt-concentration difference within a fairly narrow range of ratios of nano-channel height to the Debye screening length. The diffusion permeability of charged nano-channels to single salts is demonstrated (for the first time) to be typically larger than that of neutral nano-channels of the same dimensions due to electrical facilitation of salt diffusion.     

Plasmonic approach to enhanced fluorescence for applications in biotechnology and the life sciences

One of the most rapidly growing areas of physics and nanotechnology is concerned with plasmonic effects on the nanometer scale; these have applications in sensing and imaging technologies. Nanoplasmonic colloids such as Ag and Au have been attracting active interest, and there has been a recent explosion in the use of these metallic nanostructures to modify the spectral properties of fluorophores favorably and to enhance the fluorescence emission intensity. In this feature article, we summarize our work over a range of nanoplasmonics-assisted biological applications such as flow cytometry, immunoassays, cell imaging and bioassays where we use custom-designed plasmonic nanostructures (Ag and Au) to enhance fluorescence signatures. This fluorophore-metal effect offers unique advantages in providing improved photostability and enhanced fluorescence signals. We discuss the plasmonic enhancement of lanthanide fluorophores whose long and microsecond lifetimes offer the advantage of background-free fluorescence detection, but low photon cycling rates lead to poor brightness. We also show that plasmonic colloids are capable of enhancing the emission of fluorescent nanoparticles, including upconverting nanocrystals and lanthanide nanocomposites.     

An in situ approach for nickel-catalyzed cycloaddition

A convenient method for preparing pyridines from air-stable, commercially available catalyst precursors is described. The addition of n-BuLi to Ni(acac)2 and an NHC salt (such as IPr.HCl or SIPr.HCl) rapidly generates an active Ni0/NHC catalyst for the cycloaddition of diynes and nitriles that affords pyridines without a decrease in observed yields. The in situ method also converts diynes and carbon dioxide to the corresponding pyrones.     

A fundamental parameters approach including scattered radiation for mono-energetically excited samples in energy-dispersive x-ray fluorescence spectrometry

A fundamental parameters approach that incorporates data on scattered radiation is shown to be a useful tool for the determination of trace elements in light matrices. For thick, transparent samples, a computer program is developed that uses differetial intensity equations adjusted for decreasing geometric efficiency. Various organic and biological reference materials are analysed to assess the reliability of the procedure. A nested design for analysis of variance shows that major errors can originate from the deconvolution process and sample inhomogeneities in many cases. For loose powders, great care must be exercised to avoid errors caused by scatter from the sample cups. The program is also useful for alloys.