Structure and ultrafast dynamics of white-light-emitting CdSe nanocrystals.

White-light emission from ultrasmall CdSe nanocrystals offers an alternative approach to the realization of solid-state lighting as an appealing technology for consumers. Unfortunately, their extremely small size limits the feasibility of traditional methods for nanocrystal characterization. This paper reports the first images of their structure, which were obtained using aberration-corrected atomic number contrast scanning transmission electron microscopy (Z-STEM). With subangstrom resolution, Z-STEM is one of the few available methods that can be used to directly image the nanocrystal's structure. The initial images suggest that they are crystalline and approximately four lattice planes in diameter. In addition to the structure, for the first time, the exciton dynamics were measured at different wavelengths of the white-light spectrum using ultrafast fluorescence upconversion spectroscopy. The data suggest that a myriad of trap states are responsible for the broad-spectrum emission. It is hoped that the information presented here will provide a foundation for the future development and improvement of white-light-emitting nanocrystals.

MeltDB: a software platform for the analysis and integration of metabolomics experiment data.

MOTIVATION: The recent advances in metabolomics have created the potential to measure the levels of hundreds of metabolites which are the end products of cellular regulatory processes. The automation of the sample acquisition and subsequent analysis in high-throughput instruments that are capable of measuring metabolites is posing a challenge on the necessary systematic storage and computational processing of the experimental datasets. Whereas a multitude of specialized software systems for individual instruments and preprocessing methods exists, there is clearly a need for a free and platform-independent system that allows the standardized and integrated storage and analysis of data obtained from metabolomics experiments. Currently there exists no such system that on the one hand supports preprocessing of raw datasets but also allows to visualize and integrate the results of higher level statistical analyses within a functional genomics context. RESULTS: To facilitate the systematic storage, analysis and integration of metabolomics experiments, we have implemented MeltDB, a web-based software platform for the analysis and annotation of datasets from metabolomics experiments. MeltDB supports open file formats (netCDF, mzXML, mzDATA) and facilitates the integration and evaluation of existing preprocessing methods. The system provides researchers with means to consistently describe and store their experimental datasets. Comprehensive analysis and visualization features of metabolomics datasets are offered to the community through a web-based user interface. The system covers the process from raw data to the visualization of results in a knowledge-based background and is integrated into the context of existing software platforms of genomics and transcriptomics at Bielefeld University. We demonstrate the potential of MeltDB by means of a sample experiment where we dissect the influence of three different carbon sources on the gram-negative bacterium Xanthomonas campestris pv. campestris on the level of measured metabolites. Experimental data are stored, analyzed and annotated within MeltDB and accessible via the public MeltDB web server. AVAILABILITY: The system is publicly available at http://meltdb.cebitec.uni-bielefeld.de.

Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner-Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis.

The well-studied plant pathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) synthesizes the biotechnologically important polysaccharide xanthan gum, which is also regarded as a virulence factor in plant interactions. In Xcc, sugars like glucose are utilized as a source to generate energy and biomass for growth and pathogenicity. In this study, we used [1-(13)C]glucose as a tracer to analyze the fluxes in the central metabolism of the bacterium growing in a minimal medium. (13)C-Metabolic flux analysis based on gas chromatography-mass spectrometry (GC-MS) confirmed the prevalent catabolic role of the Entner-Doudoroff pathway. Comparative nuclear magnetic resonance (NMR)-based isotopologue profiling of a mutant deficient in glycolysis gave evidence for a moderate flux via glycolysis in the wild-type. In addition to reconfirming the Entner-Doudoroff pathway as a catabolic main route, this approach affirmed a numerically minor but important flux via the pentose phosphate pathway.

Low molecular weight plant extract induces metabolic changes and the secretion of extracellular enzymes, but has a negative effect on the expression of the type-III secretion system in Xanthomonas campestris pv. campestris.

Xanthomonas campestris pathovar campestris (Xcc) is a plant pathogenic bacterium and as such has to adapt to a variety of environments. During the course of disease, Xcc colonizes the surface of its host, infects the xylem in the early stages, and develops a fully saprophytic life-style, aided by secreted degradative enzymes, in the late stages. To get some insight into this complex regulation, Xcc was cultivated in the presence of low molecular weight host plant extract (<10 kDa). From this experiments it could be observed, that malate and sucrose are taken up preferably in such an environment. Furthermore, it was demonstrated, that the plant extract has a negative effect on the gene expression of the hrp-gene cluster, although the activator hrpG was induced. Also, the secretion of degradative enzymes was shown to be upregulated. These observations indicate, that a low molecular weight plant extract (<10 kDa) is a sufficient signal to regulate metabolic pathways and the secretion of enzymes relevant for the development of virulence in Xanthomonas, but has a negative effect on the expression of genes involved in type-III secretion.

Homogeneously alloyed CdSxSe1-x nanocrystals: synthesis, characterization, and composition/size-dependent band gap.

Alloy nanocrystals provide an additional degree of freedom in selecting desirable properties for nanoscale engineering because their physical and optical properties depend on both size and composition. We report the pyrolytic synthesis of homogeneously alloyed CdS(x)Se(1-x) nanocrystals in all proportions. The nanocrystals are characterized using UV-visible absorption spectroscopy, transmission electron microscopy, X-ray diffractrometry, and Rutherford backscattering spectrometry to determine precisely structure, size, and composition. The dependence of band gap on nanocrystal size and composition is elucidated, yielding a bowing constant of 0.29, in agreement with bulk values. In addition, the morphology of the resultant nanocrystals can be altered by changing the reaction conditions, generating structures ranging from homogeneous, spherical nanocrystals to one-dimensional gradient nanorods.