A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies.

The rapid development of next generation sequencing technology has greatly increased the amount of available microbial genomes. As a result of this development, there is a rising demand for fast and automated approaches in analyzing these genomes in a comparative way. Whole genome sequencing also bears a huge potential for obtaining a higher resolution in phylogenetic and taxonomic classification. During the last decade, several software tools and platforms have been developed in the field of comparative genomics. In this manuscript, we review the most commonly used platforms and approaches for ortholog group analyses with a focus on their potential for phylogenetic and taxonomic research. Furthermore, we describe the latest improvements of the EDGAR platform for comparative genome analyses and present recent examples of its application for the phylogenomic analysis of different taxa. Finally, we illustrate the role of the EDGAR platform as part of the BiGi Center for Microbial Bioinformatics within the German network on Bioinformatics Infrastructure (de.NBI).

Combined image interpretation of computed tomography and hybrid PET in head and neck cancer.

AIM: Evaluation of potential synergistic effects of combined image interpretation of FDG PET using a gamma camera modified for coincidence detection (hybrid PET) and computed tomography (CT) and comparison of the diagnostic accuracy of hybrid PET and dedicated PET in patients with head and neck cancer. METHODS: Forty-two patients with suspected primary or recurrent cancer were included. Twenty-four patients underwent dedicated PET in addition to attenuation-corrected hybrid PET using a one-day protocol. RESULTS: Sensitivity, specificity and accuracy for detection of primary or recurrent head and neck cancer were 74, 73, and 74% for hybrid PET, 52, 82, and 60% for CT and 77, 82, and 79% for combined reading. With the combination of CT and hybrid PET all cases of recurrent disease were detected. The largest tumour not detected was 1.7 cm in diameter. Sensitivity, specificity and accuracy for the detection of neck sides with lymph node metastases were 69, 88, and 85% for hybrid PET, 62, 88, and 84% for CT, 69, 99, and 94% for combined image interpretation. With combined interpretation four involved neck sides were missed including two cases of microscopic metastases. Hybrid PET revealed concordant results to dedicated PET in all patients with respect to the detection of primary or recurrent tumour and in 45 of 48 neck sides (94%) with the same number of false negative findings. CONCLUSION: The combination of functional information of hybrid PET and morphological information of CT by the simple approach of combined image interpretation improves the sensitivity for the detection of primary/recurrent head and neck cancer and increases the specificity of lymph node staging compared to CT alone. The accuracy of hybrid PET and dedicated PET was almost identical.

Determination of lead in blood by hydrodynamic voltammetry in a flow injection system with wall-jet detector.

Lead is one of the most widely distributed toxic heavy metals in the environment. It is a cumulative poison, affecting the brain and nervous system. The threshold between the normal lead level and the level where physiological effects become manifest is relatively narrow. It is therefore desirable to screen exposed populations in order to identify the danger in time. The lead concentration in the blood is a measure to the total amount of lead in the body. A fast, accurate and cheap method for the determination of lead in blood is therefore needed. The conventional method used to determine lead in blood is atomic absorption. Electrochemical methods like stripping voltammetry combine high analytical sensitivity with relatively low cost for the equipment; however, electrode preparation is critical for the success of an analysis, and highly skilled personnel are needed. We describe an automated electrochemical method, using flow injection analysis with a wall-jet detector. Lead is released from its binding site in the blood by ion exchange and quantified by stripping voltammetry with a mercury film electrode (MFE). The method allows for the detection of 0.05 ppm Pb(2+) with an accuracy of about 10%. Electrode poisoning by proteins from the blood can be effectively suppressed when a MFE modified with a Nafion(R)-membrane coating is used. Such modified electrodes can be activated in the solution without further treatment, and used for more than 100 analyses before they have to be replaced. A solid matrix MFE with a Nafion(R)-membrane and all necessary chemicals for mercury film formation and lead release has been developed. Such electrodes are discussed as disposable electrodes for a portable blood lead detector.

Temperature programmed decomposition (TPDE) of [Mo(CO)(6)] on metal oxide supports: a novel tool to elucidate surface acidity and surface-mediated reactions.

A novel technique, the temperature programmed decomposition (TPDE) of [Mo(CO)(6)], has been developed to examine surface acid/base properties. In particular, the nucleophility of different surface hydroxyl groups can be quantified with this method, and it is found that the activation energy for decarbonylation of the carbonyl complex correlates well with the field strength of the metal cations in the support. Activation energies are derived from the CO peak maxima in the TPDE spectra by means of the Redhead equation. TPDE is also used to probe surface-mediated reactions of metal carbonyls. The technique enables identification of intermediates formed during the thermal decomposition process. Comparison with simulated TPDE spectra provides evidence for cluster formation during decarbonylation. By quantifying the amounts of CO and H(2) generated during the TPDE reaction, the surface concentration of the adsorbed species and the oxidation state of the central atom can be deduced at any given temperature.

Catalytic CO oxidation over manganese-containing perovskites.

Mixed metal oxides are discussed as possible substitutes for noble metals in automobile catalytic converters. The catalytic activity for CO oxidation of LaMnO3 and La0.5Sr0.5MnO3 catalysts was examined.The ability of these catalysts to provide lattice oxygen and to sustain the oxidation reaction, even in the absence of molecular oxygen, has been confirmed. Measurements were performed of the reversible oxygen uptake on the two catalysts.