, 2010). GeneChip® data for biological replicates were normalized, averaged, and analyzed using GeneSpring GX 7.3 Analysis Platform software (Agilent Technologies, Redwood City, CA), as previously described (Anderson et al., 2006). Genes that exhibited ≥ twofold increase in transcript titer in response to growth phase or growth in human serum in comparison with cells grown in control conditions were determined to be ‘present’ by Affymetrix algorithms during the induced condition and that demonstrated a significant change in expression (t-test P cutoff of ≤ 0.05) where considered differentially expressed. At least two biological replicates
were included in each analysis. To confirm GeneChip® results, primer sets (Table 1) were designed for selected ORFs to measure RNA expression by RT-PCR. RNA was isolated and purified from LB cultures of A. baumannii ATCC 17978 and 98-37-09 cells Ibrutinib mouse Y-27632 clinical trial at exponential or stationary phase of growth, as described above. Forty nanograms of purified RNA from each sample was serially diluted (twofold) and subjected to RT-PCR using the AccessQuick™ RT-PCR System (Promega, Madison, WI) in a GeneAmp PCR System 9700 thermocycler (Applied Biosystems, Austin, TX) using the following parameters:
reverse transcription at 45 °C for 45 min, amplification of cDNA at 94 °C for 2 min, then 30 cycles of (94 °C for 30 s, 56 °C for 30 s, and 68 °C for 1 min), ending with a final extension at 68 °C for 7 min. For primer sets requiring lower stringency 45 or 52 °C was substituted for the Cyclic nucleotide phosphodiesterase 56 °C during PCR amplification. RT-PCR products were visualized by electrophoresis in a 2% agarose gel (UltraPure Agarose; Invitrogen, Carlsbad, CA) and ethidium
bromide staining (Thermo Scientific). Acinetobacter baumannii strains were cultured overnight in LB medium and then used to inoculate a 96-well round bottom plate with 100 μL per well of LB or 100% serum containing various concentrations of minocycline (0.25–2 μg mL−1) to a final bacterial concentration of 105 colony-forming units (CFUs) mL−1. Cultures were grown at 37 °C for 48 h. After 48 h, cultures were serially diluted in PBS and plated to enumerate CFUs mL−1 on LB agar. Assays including the efflux inhibitor phenylalanine arginine beta-naphthylamide (PAβN; Sigma) were performed as described above, except that each well also contained 60 μg mL−1 PAβN. It is well established that the expression patterns of bacterial genes, including many virulence factors, dramatically change as cells transition from exponential to stationary phase of growth. Despite its importance as an emerging bacterial pathogen, no studies have comprehensively assessed the growth phase-dependent changes in A. baumannii gene expression. Thus, we initially set out to define and compare the expression profiles of two genetically diverse A. baumannii strains, ATCC 17978 and 98-37-09, during exponential and stationary phases of growth in laboratory medium.