Project description:Ehrlichia chaffeensis is an obligatory intracellular organism, and causes human monocytic ehrlichiosis (HME), a tick-borne illness. Clinical signs of HME vary from asymptomatic infection to severe mobility that requires hospitalization or death. After whole genome sequencing of this bacterium, 425 open reading frames (38%) of 1115 in the genome were found as hypothetical gene with unknown function. A little is known about pathogenicity gene(s) and strain variation of this bacterium to date. Previously several E. chaffeensis strains were shown to be different based on comparison of limited gene sequences (p120, OMP-1[p28]s, and VLPT). To elucidate strain genetic variations and associated virulency, we carried out comparative genome hybridization (CGH) of E. chaffeensis Arkansas, Wakulla and Liberty strains, since these strains are most distinct in the previous studies. The tiling array containing approximately 300,000 probes of 29 nt spaced as dense as 8 bp on both strands of the genome of E. chaffeensis Arkansas was used. Keywords: Comparative genome hybridization
Project description:The analysis of (trace) contaminants in environmental samples represents an important tool for exposure assessment and for the evaluation of potential risks to human health. Currently, mass spectrometric detection using triple quadrupole (TQMS) systems is the established method of choice. However, screening methods using high resolution mass spectrometry (HRMS) find increasing application as they provide advantages such as enhanced selectivity. A complex composition of environmental samples is known to have enormous effects on mass analyzers. The present work therefore compares the impact of a highly matrix-loaded sample material like house-dust on the performance of mass spectrometric detection of the emerging indoor contaminant group of mycotoxins by quadrupole time-of-flight (QTOF) and TQMS after ultrahigh-performance liquid chromatographic separation. Furthermore, the role of ionization efficiencies of different ion sources in instrument sensitivity was compared using an electrospray ionization source and a newly developed heated electrospray ion source (Bruker VIP-HESI) during QTOF experiments. Finally, it was evaluated whether an additional dimension of separation enables increased sensitivity in QTOF-HRMS detection by applying mycotoxins in house-dust to an (trapped) ion mobility spectrometry instrument. The sensitivity of the QTOF detection was positively influenced by the application of the VIP-HESI ion source, and overall HRMS instruments provided enhanced selectivity resulting in simplified data evaluation compared to the TQMS. However, all performed experiments revealed strong signal suppression due to matrix components. QTOF results showed more severe effects, enabling a more sensitive detection of mycotoxins in house-dust by applying TQMS detection.
Project description:In this study two genome-reduced Bacillus subtilis strains lacking about 36% of dispensable genetic information were constructed using a markerless and scarless deletion method. In order to analyze the consequences of the deletions for the bacteria, a multi-omics characterization of the reference strain Δ6 (Westers et al., 2003; PMID 12949151) and the two deletion strains was carried out. Bacteria were cultivated in complex medium supplemented with glucose, and samples of the same cultures were subjected to metabolome, proteome, and transcriptome analyses.These revealed a massive re-organization of metabolism as well as substantial changes in the transcriptome and the proteome.