Fixed mandibles were decalcified in 5% formic acid/10% citrate, and embedded in paraffin. The entire mandible was sectioned at 6 μm/section, and every fifth section was stained with haematoxylin & eosin

to identify the lesion area. Images of the stained sections were obtained with a dissecting microscope and imported into IQBase software (Mediacybernetics, Bethesda, MD). Bone loss in appropriate sections was estimated by measuring the distance from p38 MAPK phosphorylation the first molar proximal root surface to the closest bone edge at the bottom of the root and on both sides using the measurement functions in IQBase. These numbers were obtained for all stained sections spanning the base of the root (four to six sections), and averaged. Neutrophils were identified with antibody 7/418 (AbD Serotec, Raleigh, NC) at 0·22 μg/ml, and macrophages with F4/8019 (Harlan) at 1 : 10; both were detected with biotinylated goat anti-rat antibody and the Vector ELITE ABC kit (Vector selleck chemicals Laboratories, Burlingame, CA). Osteoclasts were identified using a rabbit antiserum to cathepsin

K, as previously described.20 No primary controls were included in each experiment, and there was no reactivity of the secondary antibodies alone. Semi-quantitative estimates of phagocyte accumulation in tissue sections were obtained by measuring the area of intense staining using ImageJ or IQBase: in 3-day samples, the root canal of infected mice stained strongly for neutrophils, and the neutrophil accumulation was estimated by measurement of the length of the pulp chamber occupied by neutrophils. Nabilone One to two micrograms RNA prepared from bone blocks (approx. 5 mm3, containing the infected molar and associated bone, from which gingival tissue was removed) was reverse transcribed using standard techniques; for each sample a control reaction was performed without reverse transcriptase. Complementary DNA (cDNA) was subjected to qPCR using primers at 200–300 μm and Sybr green technology in a total volume of 20 μl. Master mix was either purchased from BioRad

(Hercules, CA) or was home-made21 using standard Taq polymerase (NE Biolabs, Ipswich, MA). For each assay, standards were prepared by amplifying a DNA fragment encompassing the qPCR primer sites: this fragment was purified, quantified and used for absolute quantification. Results, in molecules/μl were divided by the geometric mean of results from two control genes: glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and EF1a1,22 to give relative expression. Primers (Invitrogen) for IL-1α, IL-1β, IFN-γ, IL-10 and IL-12p40 were described in Akilesh et al.23 Receptor activator of nuclear factor κB ligand (RANKL) primers are described elsewhere.20 Other primers used were GAPDH: left: 5′-CGAAGGTGGAAGAGTGGGAG-3′; right: 5′-TGAAGCAGGCATCTGAGGG-3′; EF1a1: left: 5′-GGAAA TTCGAGACCAGCAAA-3′; right: 5′-ACACCAGC AGCAACAATCAG-3′; neutrophil elastase: left: 5′-TGTGAACGGCCTAAATTTCC-3′; right: 5′-GGTCAAAG CCATTCTCGAAG-3′.