Project description:The transcription factor CrzA influences cell wall organization in the pathogenic fungus Aspergillus fumigatus, and also binds to the promoter regions of chitin synthase genes upon exposure to the antifungal drug caspofungin. To gain an overview of the genes directly regulated by CrzA, the CrzA binding sites were determined genome-wide by ChIP-seq
Project description:Genomic DNA from five strains, Aspergillus fumigatus Af71, Aspergillus fumigatus Af294, Aspergillus clavatus, Neosartorya fenneliae, and Neosartorya fischeri, were co-hybridized with that of Aspergillus fumigatus Af293 and compared.
Project description:miRNAs are excellent tumor biomarkers because of their cell-type specificity and abundance. However, many miRNA detection methods, such as real-time (RT)-PCR, obliterate valuable visuospatial information in tissue samples. To enable miRNA visualization in formalin-fixed paraffin-embedded (FFPE) tissues, we developed multicolor miRNA fluorescence in situ hybridization (FISH). For proof-of-concept, we differentiated two skin tumors, namely Basal cell carcinoma (BCC) and Merkel cell carcinoma (MCC), with overlapping histologic features but distinct cellular origins. Using sequencing-based miRNA profiling and discriminant analysis, we identified tumor-specific miRNAs (miR-205 and miR-375) in BCC and MCC respectively. We addressed three major shortcomings in miRNA FISH, identifying optimal conditions for miRNA fixation and rRNA retention using model compounds and HPLC analyses, enhancing signal amplification and detection by increasing probe-hapten linker lengths, and improving probe specificity using shortened probes with minimal rRNA sequence complementarity. We validated our method on 4 BCC and 12 MCC tumors. Amplified miR-205 and miR-375 signals were normalized against directly detectable reference rRNA signals. Tumors were classified using pre-defined cut-off values; all were correctly identified in blinded analysis. We established a reliable miRNA FISH technique for parallel visualization of differentially expressed miRNAs in FFPE tumor tissues
Project description:This SuperSeries is composed of the following subset Series: GSE9275: A tri-species Aspergillus array (nidulans arrays) GSE9276: A tri-species Aspergillus array (niger arrays) GSE9277: A tri-species Aspergillus array (oryzae arrays) Keywords: SuperSeries Refer to individual Series
Project description:The full genome sequencing of the filamentous fungi Aspergillus nidulans, Aspergillus niger and Aspergillus oryzae has opened the possibilities for studying the cellular physiology of these fungi on a systemic level. As a tool to explore this, we are presenting an Affymetrix GeneChip developed for transcriptome analysis of any of the three above-mentioned aspergilli. Transcriptome analysis of triplicate batch cultivations of all three aspergilli on glucose-and xylose media has been performed, and used to validate the performance of the micro array. By doing gene comparisons of all three species, and cross-analysing this with the expression data, 23 genes, including the xylose transcriptional activator XlnR, have been identified to be a conserved response across the Aspergillus sp. Promoter analysis of the upregulated genes in all three species suggest the XlnR-binding site to be 5’-GGNTAAA-3’. We are thus presenting a validated tool for transcription analysis of three Aspergillus species and a methodology for comparative transcriptomics. Keywords: Physiological response
