Balancing inflammatory, lipid, and xenobiotic signaling pathways by VSL#3, a biotherapeutic agent, in the treatment of inflammatory bowel disease.

BACKGROUND: The interleukin 10 knockout mouse (IL10-KO) is a model of human inflammatory bowel disease (IBD) used to study host microbial interactions and the action of potential therapeutics. Using Affymetrix data analysis, important signaling pathways and transcription factors relevant to gut inflammation and antiinflammatory probiotics were identified. METHODS: Affymetrix microarray analysis on both wildtype (WT) and IL10-KO mice orally administered with and without the probiotic VSL#3 was performed and the results validated by real-time polymerase chain reaction (PCR), immunocytochemistry, proteomics, and histopathology. Changes in metabolically active bacteria were assessed with denaturing gradient gel electrophoresis (DGGE). RESULTS: Inflammation in IL10-KO mice was characterized by differential regulation of inflammatory, nuclear receptor, lipid, and xenobiotic signaling pathways. Probiotic intervention resulted in downregulation of CXCL9 (fold change [FC] = -3.98, false discovery rate [FDR] = 0.019), CXCL10 (FC = -4.83, FDR = 0.0008), CCL5 (FC = -3.47, FDR = 0.017), T-cell activation (Itgal [FC = -4.72, FDR = 0.00009], Itgae [FC = -2.54 FDR = 0.0044]) and the autophagy gene IRGM (FC = -1.94, FDR = 0.01), a recently identified susceptibility gene in human IBD. Consistent with a marked reduction in integrins, probiotic treatment decreased the number of CCL5+ CD3+ double-positive T cells and upregulated galectin2, which triggers apoptosis of activated T cells. Importantly, genes associated with lipid and PPAR signaling (PPARalpha [FC = 2.36, FDR = 0.043], PPARGC1alpha [FC = 2.58, FDR = 0.016], Nr1d2 [FC = 3.11, FDR = 0.0067]) were also upregulated. Altered microbial diversity was noted in probiotic-treated mice. CONCLUSIONS: Bioinformatics analysis revealed important immune response, phagocytic and inflammatory pathways dominated by elevation of T-helper cell 1 type (TH1) transcription factors in IL10-KO mice. Probiotic intervention resulted in a site-specific reduction of these pathways but importantly upregulated PPAR, xenobiotic, and lipid signaling genes, potential antagonists of NF-kappaB inflammatory pathways.

NuGO contributions to GenePattern.

NuGO, the European Nutrigenomics Organization, utilizes 31 powerful computers for, e.g., data storage and analysis. These so-called black boxes (NBXses) are located at the sites of different partners. NuGO decided to use GenePattern as the preferred genomic analysis tool on each NBX. To handle the custom made Affymetrix NuGO arrays, new NuGO modules are added to GenePattern. These NuGO modules execute the latest Bioconductor version ensuring up-to-date annotations and access to the latest scientific developments. The following GenePattern modules are provided by NuGO: NuGOArrayQualityAnalysis for comprehensive quality control, NuGOExpressionFileCreator for import and normalization of data, LimmaAnalysis for identification of differentially expressed genes, TopGoAnalysis for calculation of GO enrichment, and GetResultForGo for retrieval of information on genes associated with specific GO terms. All together, these NuGO modules allow comprehensive, up-to-date, and user friendly analysis of Affymetrix data. A special feature of the NuGO modules is that for analysis they allow the use of either the standard Affymetrix or the MBNI custom CDF-files, which remap probes based on current knowledge. In both cases a .chip-file is created to enable GSEA analysis. The NuGO GenePattern installations are distributed as binary Ubuntu (.deb) packages via the NuGO repository.

[Improving venous tolerance of methohexital]. / Zur Verbesserung der Venenverträglichkeit von Methohexital.

As there are still contradictions in the literature on the efficacy of different solvents to reduce venous pain after the injection of methohexital we restudied this problem. In an earlier investigation normal saline proved superior to distilled water. We now found that injection of an opioid prior to methohexital and addition of lidocaine to the methohexital solution leads to a strong reduction in the incidence of pain.