In molecular diagnosis of infectious diseases often more than 1 pathogen has to be considered. As a consequence, a series of labor-intensive and time-consuming polymerase chain reaction (PCR) approaches specific for different putative pathogens have to be carried out. To speed up diagnosis, we established a low-density microarray for simultaneous detection of diverse putative pathogens causing a disease such as granulomatous lymphadenitis. Nucleic acids from formalin-fixed, paraffin-embedded tissues of 68 patients with lymphadenitis were used for molecular diagnosis of individual pathogens by either nested single-assay PCR or 1-step multiplex PCR in combination with low-densitiy microarray hybridization. Multiplex PCR amplicons hybridized to glass slides containing probes from Mycobacterium spp., Yersinia spp., Bartonella henselea, Toxoplasma gondii, and other pathogens showed specific and reproducible signals on the array. Our results show that microarray technology combined with multiplex PCR is a promising and time-saving tool in molecular pathology of infectious diseases, allowing sensitive, simultaneous analyses of different pathogens.

Regulatory changes in genes involved in reproduction are thought to be prime targets for divergence during speciation, since they are expected to play an important role in sexual selection and sexual conflict. We used microarray analysis of RNA from different wild populations of house mouse subspecies (including Mus m. musculus, Mus m. domesticus, and Mus m. castaneus) and from the sister species Mus spretus to test this assumption. A comparison of expression divergence in brain, liver/kidney, and testis shows a major difference in the evolutionary dynamics of testis-related genes. While the comparison between species confirms an excess in divergence in testis genes, we find that all comparisons between subspecies yield only a very small number of genes with significantly different expression levels in the testis. These results suggest that the early phase of the speciation process may not be driven by regulatory changes in genes that are potential targets of sexual selection, and that the divergence in these genes is only established during a later phase of the speciation process.

Differential gene expression of Dictyostelium discoideum after infection with Legionella pneumophila was investigated using DNA microarrays. Investigation of a 48 h time course of infection revealed several clusters of co-regulated genes, an enrichment of preferentially up- or downregulated genes in distinct functional categories and also showed that most of the transcriptional changes occurred 24 h after infection. A detailed analysis of the 24 h time point post infection was performed in comparison to three controls, uninfected cells and co-incubation with Legionella hackeliae and L. pneumophilaDeltadotA. One hundred and thirty-one differentially expressed D. discoideum genes were identified as common to all three experiments and are thought to be involved in the pathogenic response. Functional annotation of the differentially regulated genes revealed that apart from triggering a stress response Legionella apparently not only interferes with intracellular vesicle fusion and destination but also profoundly influences and exploits the metabolism of its host. For some of the identified genes, e.g. rtoA involvement in the host response has been demonstrated in a recent study, for others such a role appears plausible. The results provide the basis for a better understanding of the complex host-pathogen interactions and for further studies on the Dictyostelium response to Legionella infection.

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The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.

BioTechniquesVol. 33, No. 4 BenchmarkOpen AccessComparison of Probe Preparation Methods for DNA MicroarraysPatrick Farbrother, Silke Müller, Angelika A. Noegel & Ludwig EichingerPatrick FarbrotherUniversity of Cologne, Köln, Germany, Silke MüllerUniversity of Cologne, Köln, Germany, Angelika A. NoegelUniversity of Cologne, Köln, Germany & Ludwig Eichinger*Address correspondence to: Dr. Ludwig Eichinger, Institute for Biochemistry I, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Köln, Germany. e-mail: E-mail Address: ludwig.eichinger@uni-koeln.deUniversity of Cologne, Köln, GermanyPublished Online:17 Sep 2018https://doi.org/10.2144/02334mt01AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit FiguresReferencesRelatedDetailsCited ByDictyostelium transcriptional host cell response upon infection with LegionellaCellular Microbiology, Vol. 8, No. 3Dictyostelium as host model for pathogenesisCellular Microbiology, Vol. 7, No. 3Current Awareness on Comparative and Functional GenomicsComparative and Functional Genomics, Vol. 4, No. 2 Vol. 33, No. 4 Follow us on social media for the latest updates Metrics Downloaded 107 times History Published online 17 September 2018 Published in print October 2002 Information© 2018 Author(s)PDF download