A non-MRA C^r Frame Wavelet with Rapid Decay

A generalized filter construction is used to build an example of a non-MRA normalized tight frame wavelet for dilation by 2 in . This example has the same multiplicity function as the Journé wavelet, yet has a Fourier transform and can be made to be for any fixed postive integer . L. Baggett and P. Jorgensen were supported by a US–NSF Focused Research Group (FRG) grant.     

Latent models for cross-covariance

We consider models for the covariance between two blocks of variables. Such models are often used in situations where latent variables are believed to present. In this paper we characterize exactly the set of distributions given by a class of models with one-dimensional latent variables. These models relate two blocks of observed variables, modeling only the cross-covariance matrix. We describe the relation of this model to the singular value decomposition of the cross-covariance matrix. We show that, although the model is underidentified, useful information may be extracted. We further consider an alternative parameterization in which one latent variable is associated with each block, and we extend the result to models with r-dimensional latent variables.     

Discrimination of Isomers of Released <Emphasis Type="Italic">N-</Emphasis> and <Emphasis Type="Italic">O-</Emphasis>Glycans Using Diagnostic Product Ions in Negative Ion PGC-LC-ESI-MS/MS

Profiling cellular protein glycosylation is challenging due to the presence of highly similar glycan structures that play diverse roles in cellular physiology. As the anomericity and the exact linkage type of a single glycosidic bond can influence glycan function, there is a demand for improved and automated methods to confirm detailed structural features and to discriminate between structurally similar isomers, overcoming a significant bottleneck in the analysis of data generated by glycomics experiments. We used porous graphitized carbon-LC-ESI-MS/MS to separate and detect released N- and O-glycan isomers from mammalian model glycoproteins using negative mode resonance activation CID-MS/MS. By interrogating similar fragment spectra from closely related glycan isomers that differ only in arm position and sialyl linkage, product fragment ions for discrimination between these features were discovered. Using the Skyline software, at least two diagnostic fragment ions of high specificity were validated for automated discrimination of sialylation and arm position in N-glycan structures, and sialylation in O-glycan structures, complementing existing structural diagnostic ions. These diagnostic ions were shown to be useful for isomer discrimination using both linear and 3D ion trap mass spectrometers when analyzing complex glycan mixtures from cell lysates. Skyline was found to serve as a useful tool for automated assessment of glycan isomer discrimination. This platform-independent workflow can potentially be extended to automate the characterization and quantitation of other challenging glycan isomers.

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Graphical Abstract ?

     

PHOTOSENSITIZATION OF HUMAN DIPLOID CELL CULTURES BY INTRACELLULAR FLAVINS AND PROTECTION BY ANTIOXIDANTS

Abstract— The damaging effects of near ultraviolet and visible light on WI-38 human diploid lung fibroblasts were investigated. WI-38 cells in culture were killed by light doses ranging from 2 to 10 × 10³ W/m² h. There was an inverse correlation between culture age, i.e. population doubling level and photosensitivity. However, this effect could not be related to capacity for DNA synthesis and cell division.
Flavins were clearly implicated as endogenous photosensitizers, and antioxidants such as d, l -α-tocopherol (vitamin E), BHT and ascorbic acid were found to afford the cells protection from light damage. Furthermore, products of lipid peroxidation could be detected in cell homogenates irradiated in the presence of ribofiavin.     

Proteomics: capacity versus utility

Until recently scientists studied genes or proteins one at a time. With improvements in technology, new tools have become available to study the complex interactions that occur in biological systems. Global studies are required to do this, and these will involve genomic and proteomic approaches. High-throughput methods are necessary in each case because the number of genes and proteins in even the simplest of organisms are immense. In the developmental phase of genomics, the emphasis was on the generation and assembly of large amounts of nucleic acid sequence data. Proteomics is currently in a phase of technological development and establishment, and demonstrating the capacity for high throughput is a major challenge. However, funding bodies (both in the public and private sector) are increasingly focused on the usefulness of this capacity. Here we review the current state of proteome research in terms of capacity and utility.     

Pulsed field-gradient spin echo N.M.R. studies of flow in fluids

An analysis is presented of the effects of various flow patterns on spin echo shapes and amplitudes in the presence of both static and pulsed gradients in the applied magnetic field. Two approaches are used, one based on the Bloch equations, the other on a molecular average picture. In the case of flow patterns with velocity gradients the effects of self-diffusion across these on the N.M.R. experiments is pointed out and shown to be negligible in most cases of interest. Extension of a multipulse sequence for the study of flow to include pulsed field gradients is outlined. Experiments are described which largely confirm the theoretical predictions (except in the case of echo shapes) for plug flow and laminar flow in a circular pipe. The problem of loss of labelled nuclei from the receiver coil during the experiment is treated in detail for the case of laminar flow. The method is applied to a brief study of the flow properties of agar gel as a function of agar concentration. It is shown by using both phase sensitive and diode detectors that the flow pattern changes from laminar at low agar concentration to a sheared plug flow at higher concentrations.     

Improved 2-DE of microorganisms after acidic extraction

2-DE separations of protein extracts sometimes have problems with poor resolution and streaking. This problem is particularly apparent with microorganisms, most notably those with a large cell wall. Here we describe a novel, rapid protocol for the extraction of microorganisms in acidic conditions, leading to increased resolution and 2-D gel quality. The efficiency of the protocol is demonstrated with extracts of bacteria, Escherichia coli and Bacillus subtilis; fungus, Trichoderma harzianum and yeast, Saccharomyces cerevisiae. We also demonstrate using a membrane centrifugal filtration, that large acidic molecules in excess of 100 kDa, probably including cell wall material, are responsible for the separation difficulties. A range of acidic extraction conditions were investigated, and it was found that optimal extraction is achieved using an extraction solution acidified to pH 3 by 80 mM citric acid. These findings have significant implications for the proteomic study of many medically, agriculturally and environmentally significant microorganisms, as the cell walls of these organisms are often considerably more complex than many commonly studied laboratory strains.     

Negative ion graphitised carbon nano-liquid chromatography/mass spectrometry increases sensitivity for glycoprotein oligosaccharide analysis

Negative ion nano-liquid chromatography/mass spectrometry (nano-LC/MS) and tandem mass spectrometry (nano-LC/MS(2)), using graphitised carbon as separating medium, were explored for analysing neutral and acidic O-linked and N-linked oligosaccharide alditols. Compared to the sensitivity of capillary LC/MS (flow rate of 6 microL/min) coupled with a conventional electrospray ionisation source, the nano-LC/MS (flow rate of 0.6 microL/min) with a nanoflow ion source was shown to increase the sensitivity ten-fold with a detection limit in the low-femtomole range. The absolute signals for the [M-nH](n-) ions of the oligosaccharides were increased 100-fold, enabling accumulation of high-quality fragmentation data in MS(2) mode, in which detection of low abundant sequence ions is necessary for characterisation of highly sialylated N-linked oligosaccharides. Oligosaccharides with high numbers of sialic acid residues gave dominant fragments arising from the loss of sialic acid, and less abundant fragments from cleavage of other glycosidic bonds. Enzymatic off-line desialylation of oligosaccharides in the low-femtomole range prior to MS(2) analysis was shown to increase the quality of the spectra. Automated glycofragment mass fingerprinting using the GlycosidIQ software confirmed the oligosaccharide sequence for both neutral desialylated as well as sialylated structures. Furthermore, the use of graphitised carbon nano-LC/MS enabled the detection of four sialylated O-linked oligosaccharides on membrane proteins from ovarian tissue (5 microg of total amount of protein).