RNA was collected by centrifugation at 18630 × g (4°C), washed with 70% ethanol and resuspended in water. Any contaminating DNA was removed by DNase digestion (Turbo-DNase, Ambion) according to the manufacturer’s instructions. Quality and quantification of ACP-196 mouse total bacterial mRNA extracted was 4SC-202 molecular weight assessed using the Experion system (Experion RNA Standard Sense Kit, Bio-Rad). Complementary DNA was synthesised from 1 μg total RNA using the Transcriptor First Strand cDNA Synthesis Kit (Roche) and random

hexamer primers (supplied) according to manufacturer’s instructions. Real-time and reverse-transcriptase PCR Real-Time PCR reactions were performed in the LightCycler version 1.5 (Roche Diagnostics) using either the LightCycler MasterPlus SYBR Green (Roche) or the Master SYBR Green kit (Roche). PCR master mixes (SYBR Green dye and FastStart Taq DNA polymerase were supplied) were prepared according to the manufacturer’s instructions. A four step experimental protocol was used: (i) activation (95°C for 15 min) (ii) amplification step

repeated for 45 cycles (95°C for 10 sec; primer-specific Tm for 10 sec, 72°C for 10 sec with a single fluorescence measurement) (iii) melting curve analysis (65°C-95°C with a heating rate of 0.1°C per second and a continuous fluorescence measurement) (iv) cooling step down to 40°C (see Table 1 for annealing temperatures). Refer to Table 5 for a complete list of NVP-LDE225 datasheet primer sequences used to analyse the genes of interest. RNA template and no-template controls were included to determine DNA contamination of RNA samples or PCR reactions. All PCR reactions as well as all biological experiments were done in triplicate. Relative quantification of gene expression was done using the REST-384 Version 1 software with PCR efficiency correction for individual real-time PCR transcripts [48]. SigA was used as the internal standard to normalise target gene expression levels in each RNA sample [59] as it has been shown that sigA expression Acyl CoA dehydrogenase remains constant

under various growth and stress conditions [60]. Table 5 Primer sequences used for the relative quantification of glutamine synthetase and glutamate dehydrogenase genes.* Gene Sense Primer (5′-3′) Antisense Primer (5′-3′) Product size (bp) Annealing Temperature (°C) glnA1 ATGTGCTGCTGTTCAAGT TGAAGGTGACGGTCTTGC 66 55 sigA GACTCGGTTCGCGCCTA CCTCTTCTTCGGCGTTG 64 55 msmeg_6272 TGATCCGCCACATCCTG GATGTAGGTGCCGATGC 65 56.5 msmeg_5442 AGATCATGCGGTTCTGTC GTGTATTCACCGATGTGCC 61 55 msmeg_4699 GTGAGGACTTCCGCACC CCGCTTGACGACGAATC 104 55 *The product size and annealing temperatures are also given. sigA was used as an internal control or housekeeping gene. Reverse transcriptase PCR reactions were carried out in the GeneAmp PCR System 9700 Reverse transcriptase PCR reactions were carried out in the GeneAmp PCR System 9700 (Applied Biosystems) using HotStar Taq DNA Polymerase (Qiagen) according to manufacturer’s instructions.