The percentage and absolute numbers of different cell types were determined by flow cytometric analysis and cell-counting beads (Life Technologies, Grand Island, NY). FACS analysis was performed using a BD Biosciences LSRII Flow cytometer and FlowJo (Tree Star, Ashland, OR) analysis software. In other JNK inhibitor experiments,

cells from blood were analysed and quantified by flow cytometry. Expression of CXCR2, CD62 ligand and CD44 on neutrophils in blood was quantified using antibodies purchased from eBioscience. C57BL/6 and MyD88−/− mice were treated with a cocktail of broad-spectrum antibiotics in their drinking water starting from birth to the time they were used in experiments as described before.[22] The antibiotic cocktail consisted of ampicillin 1 g/l, neomycin 1 g/l, metronidazole 1 g/l (Sigma-Aldrich) and vancomycin 0·5 g/l (PhytoTechnology

Laboratories, Shawnee Mission, KS). The artificial aspartame sweetener, Equal (Merisant Company, Chicago, IL) was added to the water 5 g/l to make it palatable for the mice to drink. Pups received the antibiotics indirectly via lactating mothers till they were weaned. Drinking water containing the antibiotics was replaced every week. DNA was isolated from colonic contents of MK-1775 in vitro mice by the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). The quantitative PCR primers used to amplify the bacterial 16S V2 region were sense, 5′-AGYGGCGIACGGGTGAGTAA-3′; and anti-sense, 5′-CYIACTGCTGCCTCCCGTAG-3′. Quantitative PCR primers used to amplify the housekeeping gene GAPDH were sense 5′-TGATGGGTGTGAACCACGAG-3′; and anti-sense 5′-TCAGTGTAGCCCAAGATGCC-3′. Quantitative PCR was performed using the iQ SYBR Green supermix on the CFX96 Touch Bio-Rad machine (Bio-Rad, Hercules, CA). The PCR cycling

reaction used was 15 min activation step (95°C); 35 cycles of 30 seconds denaturation (95°C), 30 seconds annealing (60°), and 30 seconds extension (72°C). Lipopolysaccharide (LPS) from Escherichia Liothyronine Sodium coli, serotype 026:B6, purified by gel-filtration chromatograph (Sigma Aldrich) was administered in the drinking water of mice at a concentration of 33 mg/l from 3 to 5 weeks of age. Tamoxifen (Sigma-Aldrich) solution was prepared in corn oil (Sigma-Aldrich) at 10 mg/ml by incubating at 37°C for 2 hr. To induce deletion of floxed genes in adult mice, tamoxifen (50 mg/kg of body weight) was administered to floxed mice by oral gavage for three alternate days. Mice were used in experiments 7 days after the last administration. For treating pups, lactating mothers were treated intraperitoneally with tamoxifen (200 mg/kg of body weight) from the day of birth for 5 consecutive days. The efficiency of deletion of floxed MyD88 allele was assessed using Taqman PCR using primers and the method described previously.[23] The PCR cycling reaction was performed on the C1000 Thermal Cycler (Bio-Rad).