2f). Mosquera and colleagues targeted invasive hyphae (Fig. 2f) as their sampled population in order to avoid filamentous necrotrophic hyphae characteristic of late-stage infection. Invading hyphae were harvested from leaf sheaths at 36 h postinfection, obtaining a relatively synchronous cell population in which most hyphae were inside first-invaded cells. Leaf sheaths were

manually dissected in order to remove uninfected plant material and infected material was snap frozen before RNA extraction. RNA amplification was integral to the labelling protocol, with 500 ng of total RNA generating 10–15 μg of labelled cRNA. All of the studies captured significant numbers of differentially expressed genes, where GSK1120212 up/downregulated gene sets consisted of 1281/897 [9075] (McDonagh et al., 2008), 58/50 [85% of arrayed spots] (Walker et al., 2009), 255/221 [787] (Thewes et al., 2007); 1120/781 [15152] (Thewes et al., 2007) and 713/423

[6750] (Kamper et al., 2006), where square parentheses indicate the numbers of assayable spots per experiment. The C. neoformans SAGE analysis returned data on 84 gene tags (normalized to every 20 000 of the tag population sequenced), showing a higher representation relative to previously documented in vitro SAGE libraries, including a low-iron Protein Tyrosine Kinase inhibitor medium (LIM) SAGE library (Hu et al., 2007) against which most comparisons were made. We used several strategies to derive multispecies information on the co-ordinate regulation of homologous genes (Table 2) including best hit blast (Altschul et al., 1990) analysis, applied in a unidirectional sense, using peptides derived from the translation of species-specific differentially regulated transcript sequences. We also matched text descriptors from gene annotations in instances where spot annotations could not be readily matched to publicly accessible annotation databases or where significant redundancy of function among

multiple gene identifiers might be expected (e.g. oxidoreductases and alcohol dehydrogenases). Despite the variance among the size of datasets and disparate infection models, some interesting observations can be drawn from the comparison. We found impressive concordance between upregulated A. fumigatus and C. neoformans genes (Table 2). Such a similarity of the transcription profile is even more remarkable, given Baricitinib the varying immunosuppressive regimens used and different morphogenetic programmes of the two species (yeast vs. filamentous fungus). This intriguing finding may therefore reflect the similarity of nutrient sources and physiological conditions (such as temperature, iron limitation and oxygen tension) in the mammalian pulmonary niche and the dominance of such factors over immune status and species-specific traits. Despite the similarities in infection modelling procedures, the progression of infection would have differed significantly between the McDonagh and Hu studies in respect of the differential pathogenic strategy adopted by A. fumigatus and C.