We report the results of a genome-wide analysis of transcription in Arabidopsis thaliana after treatment with Pseudomonas syringae pathovar tomato. Our time course RNA-Seq experiment uses over 500 million read pairs to provide a detailed characterization of the response to infection in both susceptible and resistant hosts. The set of observed differentially expressed genes is consistent with previous studies, confirming and extending existing findings about genes likely to play an important role in the defense response to Pseudomonas syringae. The high coverage of the Arabidopsis transcriptome resulted in the discovery of a surprisingly large number of alternative splicing (AS) events – more than 44% of multi-exon genes showed evidence for novel AS in at least one of the probed conditions. This demonstrates that the Arabidopsis transcriptome annotation is still highly incomplete, and that AS events are more abundant than expected. To further refine our predictions, we identified genes with statistically significant changes in the ratios of alternative isoforms between treatments. This set includes several genes previously known to be alternatively spliced or expressed during the defense response, and it may serve as a pool of candidate genes for regulated alternative splicing with possible biological relevance for the defense response against invasive pathogens.

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Future Internet architectural design has attracted much research attention recently, and many novel architectural ideas have been suggested. The software and hardware realization of these architectural vision is a complex task in itself, and is worthy of research attention. In this paper, we examine a recently proposed integration of a measurement architecture in our previously described SILO architecture, and examine alternatives in realizing this integration. We demonstrate, by actual implementation and quantitative investigation, the importance of considering realization in architectural research by showing that there are unexpected factors affecting the performance of these realizations, resulting in unintended consequences, and we identify the better alternative.