High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry

Direct injection of samples on high-resolving mass spectrometers is an effective way to maximize analytical throughput and yet allow analyte discrimination in complex samples by mass-to-charge ratio. We present a platform of flow injection electrospray-time-of-flight mass spectrometry to profile small molecules in >1400 biological extracts per day at native mass resolution. We comprehensively benchmark the performance with more than 5000 injections of chemically defined standards and Escherichia coli cellular extracts obtained from miniscale cultivations. For at least 90% of tested compounds, we attain a linear response over 3 decades of concentration, interday coefficient of variation of <20%, and a mass accuracy of <0.001 amu. In polar Escherichia coli fractions, we reproducibly detected >1500 distinct ions in each mode. The accurate mass and correlation analysis enabled one to assign with good confidence 400-800 ions to electrospray derivatives of metabolites listed in the genome-wide reconstruction of Escherichia coli metabolism. Hence, we attain a coverage of about one-quarter of the total number of compounds listed in the reconstruction. Finally, we present an exemplary screen with Escherichia coli deletion mutants to show the exquisite capacity of the platform to identify lesions in primary metabolism at high throughputs.     

A suffix tree approach to anti-spam email filtering

We present an approach to email filtering based on the suffix tree data structure. A method for the scoring of emails using the suffix tree is developed and a number of scoring and score normalisation functions are tested. Our results show that the character level representation of emails and classes facilitated by the suffix tree can significantly improve classification accuracy when compared with the currently popular methods, such as naive Bayes. We believe the method can be extended to the classification of documents in other domains. Editor: Tom Fawcett     

Mathematical model of an industrial robot with articulated configuration and six degrees of freedom

This paper analyses the load influence on a d.c. drive motor servo system for all six degrees of freedom of industrial robots with an articulated configuration. Through the analyses, the analytical equations of total inertia and gravitation moments of an industrial robot servo system for external coordinate function were obtained. A mathematical model of an electro-mechanical industrial robot system was also developed.     

Digital PCR Panel for Sensitive Hematopoietic Chimerism Quantification after Allogeneic Stem Cell Transplantation

Accurate and sensitive determination of hematopoietic chimerism is a crucial diagnostic measure after allogeneic stem cell transplantation to monitor engraftment and potentially residual disease. Short tandem repeat (STR) amplification, the current “gold standard” for chimerism assessment facilitates reliable accuracy, but is hampered by its limited sensitivity (≥1%). Digital PCR (dPCR) has been shown to combine exact quantification and high reproducibility over a very wide measurement range with excellent sensitivity (routinely ≤0.1%) and thus represents a promising alternative to STR analysis. We here aimed at developing a whole panel of digital-PCR based assays for routine diagnostic. To this end, we tested suitability of 52 deletion/insertion polymorphisms (DIPs) for duplex analysis in combination with either a reference gene or a Y-chromosome specific PCR. Twenty-nine DIPs with high power of discrimination and good performance were identified, optimized and technically validated. We tested the newly established assays on retrospective patient samples that were in parallel also measured by STR amplification and found excellent correlation. Finally, a screening plate for initial genotyping with DIP-specific duplex dPCR assays was designed for convenient assay selection. In conclusion, we have established a comprehensive dPCR system for precise and high-sensitivity measurement of hematopoietic chimerism, which should be highly useful for clinical routine diagnostics.     

Novel electrode materials based on ion beam induced deposition of platinum carbon composites

Untreated and thermally annealed platinum carbon (PtC) composites obtained by ion beam induced deposition (IBID) are physically and electrochemically characterized as novel patternable electrode materials. Energy dispersive X-ray spectroscopy (EDX) and Raman spectroscopy reveal that annealing in ambient atmosphere and at temperatures above 400 °C substantially reduces the amount of carbon within the deposited material. Raman spectra also show that at elevated temperatures carbon rearranges into a more structured graphitic-like phase. Atomic force microscopy (AFM) reveals that after the annealing procedure the surface structure appears more corrugated, while the dimensions of granular surface features decreases. Furthermore, it is shown that electrodes based on annealed PtC material show an improved heterogeneous electron transfer rate for the oxidation of potassium hexacyanoferrate(II) trihydrate by almost three orders of magnitude, whereas the reduction of hexaammineruthenium(III) trichloride proceeds at similar rates for both treated and untreated electrodes. The rate of electrochemical oxidation of H₂O₂, which is influenced by the composition of the electrode surface, is also improved at thermally annealed electrodes. Finally, cyclic voltammetry in sulfuric acid shows an increase in surficial platinum concentration after annealing of the material.     

Particle Adhesion to Drops

The adhesion of spheroidal particles to spherical drops is calculated and discussed in terms of an equilibrium-penetration index. The present study emphasizes the case of particles that are sufficiently large to affect the drop volume upon penetration. It is shown that the more elongated the particles, the steeper the dependence of the penetration index on the contact angle. The effect of line tension on nanoscale particles is considered. Positive line tensions increase the steepness of the dependence of penetration index on contact angle whereas negative line tensions decrease this dependence. In addition, the energy barrier caused by positive line tensions is presented and discussed.     

π-ELECTRON CONTENTS OF RINGS IN THE DOUBLE-HEXAGONAL-CHAIN HOMOLOGOUS SERIES (PYRENE,ANTHANTHRENE AND OTHER ACENOACENES)

Abstract

Recently three methods for calculating the π-electron content of rings of benzenoid hydrocarbons were put forward: one based on the consideration of Kekuléstructural formulas, and the other two based on an analogous treatment of the Clar aromatic sextet formulas. These three methods are applied to the homologous series consisting of two condensed acene chains (whose first members are pyrene, anthanthrene, peri-naphthacenonaphthacene, …), leading to basically identical results. In contrast to acenes (in which the partition of π-electrons into rings is uniform), in the double-hexagonal-chain species the partition of π-electrons is highly non-uniform. The electron content monotonically decreases, in opposite directions, along the two acene chains, being maximal in the least annelated rings. Some other generally valid regularities in the π-electron properties of the double–hexagonal–chain benzenoids are also pointed out.     

Development of a Hypersensitive Periodate‐Cleavable Amino Acid that is Methionine‐ and Disulfide‐Compatible and its Application in MHC Exchange Reagents for T Cell Characterisation

Incorporation of cleavable linkers into peptides and proteins is of particular value in the study of biological processes. Here we describe the synthesis of a cleavable linker that is hypersensitive to oxidative cleavage as the result of the periodate reactivity of a vicinal amino alcohol moiety. Two strategies directed towards the synthesis of a building block suitable for solid‐phase peptide synthesis were developed: a chemoenzymatic route, involving L ‐threonine aldolase, and an enantioselective chemical route; these led to α,γ‐diamino‐β‐hydroxybutanoic acids in diastereoisomerically mixed and enantiopure forms, respectively. Incorporation of the 1,2‐amino alcohol linker into the backbone of a peptide generated a conditional peptide that was rapidly cleaved at very low concentrations of sodium periodate. This cleavable peptide ligand was applied in the generation of MHC exchange reagents for the detection of antigen‐specific T cells in peripheral blood cells. The extremely low concentration of periodate required to trigger MHC peptide exchange allowed the co‐oxidation of methionine and disulfide residues to be avoided. Conditional MHC reagents hypersensitive to periodate can now be applied without limitations when UV irradiation is undesired or less practical.     

Optimizing the Kinetics and Thermodynamics of DNA i‐Motif Folding

Under slightly acidic conditions, single cytidine‐rich DNA strands can form four‐stranded structures called i‐motifs. The stability of the i‐motif structure is based on the intercalation of hemiprotonated C–C⁺ base pairs. In addition, the stability of these structures is influenced by pH, temperature, salt concentration, number of cytidines per C‐rich stretch, and length of sequence; it also depends on the nucleotides in the connecting loop regions. Here, we investigated the influence of the loop nucleotides on i‐motif stability, structure, and kinetics of folding, in five structures with the same loop‐size but different adenosine and thymidine residues within the loop. The stabilities of the i‐motif structures were determined by CD melting, and structure and kinetics of folding were studied by static and time‐resolved NMR experiments.     

Simultaneous Detection of Positive and Negative Ions From Single Airborne Particles by Real-time Laser Mass Spectrometry

ABSTRACT

The instrumental setup used for simultaneous bipolar ion detection in on-line single-particle analysis by laser mass spectrometry is described. Particle size calibration has been performed using aerodynamic time-of-flight techniques. Mass spectra of several hundred ambient particles with aerodynamic diameters of 0.8 μm have been evaluated for statistical classification (Principal Components Analysis [PCA]) in order to identify main chemical components of the prominent particle classes.