Analysis of human serum by liquid chromatography-mass spectrometry: improved sample preparation and data analysis

Discovery of biomarkers is a fast developing field in proteomics research. Liquid chromatography coupled on line to mass spectrometry (LC-MS) has become a powerful method for the sensitive detection, quantification and identification of proteins and peptides in biological fluids like serum. However, the presence of highly abundant proteins often masks those of lower abundance and thus generally prevents their detection and identification in proteomics studies. To perform future comparative analyses of samples from a serum bank of cervical cancer patients in a longitudinal and cross-sectional manner, methodology based on the depletion of high-abundance proteins followed by tryptic digestion and LC-MS has been developed. Two sample preparation methods were tested in terms of their efficiency to deplete high-abundance serum proteins and how they affect the repeatability of the LC-MS data sets. The first method comprised depletion of human serum albumin (HSA) on a dye ligand chromatographic and immunoglobulin G (IgG) on an immobilized Protein A support followed by tryptic digestion, fractionation by cation-exchange chromatography, trapping on a C18 column and reversed-phase LC-MS. The second method included depletion of the six most abundant serum proteins based on multiple immunoaffinity chromatography followed by tryptic digestion, trapping on a C18 column and reversed-phase LC-MS. Repeatability of the overall procedures was evaluated in terms of retention time and peak area for a selected number of endogenous peptides showing that the second method, besides being less time consuming, gave more repeatable results (retention time: <0.1% RSD; peak area: <30% RSD). Application of an LC-MS component detection algorithm followed by principal component analysis (PCA) enabled discrimination of serum samples that were spiked with horse heart cytochrome C from non-spiked serum and the detection of a concentration trend, which correlated to the amount of spiked horse heart cytochrome C to a level of 5 pmol cytochrome C in 2 microl original serum.     

Frequency-agile,rapid scanning spectroscopy: absorption sensitivity of 2 × 10−12 cm−1 Hz−1/2 with a tunable diode laser

We present ultrasensitive measurements of molecular absorption using frequency-agile rapid scanning, cavity ring-down spectroscopy with an external-cavity diode laser. A microwave source that drives an electro-optic phase modulator with a bandwidth of 20 GHz generates pairs of sidebands on the probe laser. The optical cavity provides for high sensitivity and filters the carrier and all but a single, selected sideband. Absorption spectra were acquired by stepping the tunable sideband from mode-to-mode of the ring-down cavity at a rate that was limited only by the cavity decay time. This approach allows for scanning rates of 8 kHz per cavity resonance, a minimum detectable absorption coefficient of 1.7 × 10^?11 cm^?1 after only 20 ms of averaging, and a noise-equivalent absorption coefficient of 1.7 × 10^?12 cm^?1 Hz^?1/2. By comparison with cavity-enhanced laser absorption spectrometers reported in the literature, the present system is, to the best of our knowledge, among the most sensitive and has by far the highest spectrum scanning rate.     

Ising models with interfaces,defect lines,and walls

The transverse fluctuations of meandering interfaces in two-dimensional SOS models containing walls and defect lines may lead to a singularity in the correlation function. Corresponding Ising models below the bulk critical temperature are studied using an exact analytical transfermatrix method and Monte Carlo simulations. Typically, a rather smooth behaviour is observed in static and dynamic quantities.     

Quantized charge transport,chiral anomalies,and fractional charge

The phenomenon of quantized charge transport is studied using relativistic field theory. Perhaps surprisingly, the charge outflow per period is sometimes quantized in units of two. The interplay between quantized transport, chiral anomalies, and charge fractionization is clarified. In particular, yet another derivation of the relation between π → 2γ and γ → 3π is given.     

Renormalizing rectangles and other topics in random matrix theory

We consider random Hermitian matrices made of complex or realM×N rectangular blocks, where the blocks are drawn from various ensembles. These matrices haveN pairs of opposite real nonvanishing eigenvalues, as well asM–N zero eigenvalues (forM>N). These zero eigenvalues are kinematical in the sense that they are independent of randomness. We study the eigenvalue distribution of these matrices to leading order in the large-N, M limit in which the rectangularityr=M/N is held fixed. We apply a variety of methods in our study. We study Gaussian ensembles by a simple diagrammatic method, by the Dyson gas approach, and by a generalization of the Kazakov method. These methods make use of the invariance of such ensembles under the action of symmetry groups. The more complicated Wigner ensemble, which does not enjoy such symmetry properties, is studied by large-N renormalization techniques. In addition to the kinematical -function spike in the eigenvalue density which corresponds to zero eigenvalues, we find for both types of ensembles that if |r–1| is held fixed asN, theN nonzero eigenvalues give rise to two separated lobes that are located symmetrically with respect to the origin. This separation arises because the nonzero eigenvalues are repelled macroscopically from the origin. Finally, we study the oscillatory behavior of the eigenvalue distribution near the endpoints of the lobes, a behavior governed by Airy functions. Asr1 the lobes come closer, and the Airy oscillatory behavior near the endpoints that are close to zero breaks down. We interpret this breakdown as a signal thatr1 drives a crossover to the oscillation governed by Bessel functions near the origin for matrices made of square blocks.     

Coding and computation with neural spike trains

We study a simple model for the statistics of neural spike trains as they encode a continuously varying signal. The model is motivated with reference to several recent experiments on sensory neurons, and we show how analogies between the relevant probabilistic issues in neural coding and statistical mechanics can be exploited. Results are given for the information capacity of the code, for the optimal structure of code-reading algorithms, and for the time delays which arise in optimal processing of the coded signal. In addition, we show how simple analog computations can be expressed directly in terms of transformations of the spike train. The rules for reading the code and for optimal analog computation depend on the context for behavioral decision making-the relative weights assigned to different types of errors, the relative importance of different signals. We find that there is a conflict between minimizing this context dependence of the code and maximizing its information capacity; a compromise can be achieved by appropriate preprocessing (filtering) of the encoded signal. Experiments on auditory and visual neurons qualitatively confirm the predicted filtering. Similarly, the structure of the optimal multiplier neuron is shown to depend upon the intensity and spectral content of incoming signals, and these predictions compare favorably with experiments on a movement-sensitive cell in the fly visual system.     

The Reaction of Indole with Propiolic Acid

The reaction of indole with propiolic acid ia 1 : 1 mole ratio gave an adduct (I) of 2 : 1 addition with decarboxylation. The reaction of indole with propiolic acid methyl ester gave a 2 : 1 adduct (II). Hydrolysis of adduct II yield the corresponding carboxylic acid (IV). Decarboxylation of IV also gave I. The mechanism of title reaction were fully studied.