Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.
Project description:Bats harbour various viruses without severe symptoms and act as natural reservoirs. This tolerance of bats toward viral infections is assumed to be originated from the uniqueness of their immune system. However, how the innate immune response varies between primates and bats remains unclear. To illuminate differences in innate immune responses among animal species, we performed a comparative single-cell RNA-sequencing analysis on peripheral blood mononuclear cells (PBMCs) from four species including Egyptian fruit bats inoculated with various infectious stimuli.
Project description:The US is in the midst of a major drug epidemic fueled in large part by the widespread recreational use of syntheticopioids such as fentanyl. we evaluated the impact of fentanyl using in cell lines that replicate infectious viruses. RNAseq identified a number of hepatocyte genes that were differentially regulated by fentanyl, including those related to apoptosis, the antiviral / interferon response, chemokine signaling, and NFkB signaling.
Project description:The Virochip microarray (version 4.0) was used to detect viruses in patients from North America with unexplained influenza-like illness at the onset of the 2009 H1N1 pandemic.
