TNF and IL-12 assays For the TNF secretion assays, 2

× 105 bone marrow-derived macrophages in DMEM infection media were seeded onto each well of 12 well plates and infected with bacteria as indicated above. The culture supernatants were then collected 20 h after incubation in infection media supplemented with 100 μg/ml gentamycin. The amount of TNF in supernatants was then measured via ELISA (BD Bioscience). The RAW IL-12 promoter cell line was created and used to measure IL-12 p40 induction as described in great detail in our previous publication [12]. TLR interaction assay The Chinese hamster ovary (CHO) cells transfected with the inducible membrane protein CD25 under control of a region from the human E-selectin promoter containing nuclear fact-kB GSI-IX binding sites and expressing CD14 and either human Toll-like receptor 2 (TLR-2) or human TLF-4 were created as described in [28] kindly provided by Dr. D.T. Golenbock. Cells were used exactly as described previously by our group [12]. Apoptosis assays In most of the experiments the flow cytometry-based, hypodiploid assay was used for the detection of apoptosis after infection of bone marrow-derived macrophages and dendritic Neratinib cells. Cells were collected

after infection, pelleted and resuspended in propidium iodine (PI)/RNase buffer (BD Pharmingen) for 20 min and the percentage of hypodiploid positive cells was determined by flow cytometry in duplicates in the FL-2 channel at 580 nm (FACS-Calibur, BD Biosciences). The TUNEL assay was performed as suggested by the manufacturer (Roche) and described previously [8]. The apoptosis induction mediated by lipoglycanes was analyzed via AnnexinV-Alex488 (Molecular Probes) and PI double staining and flow cytometry as described previously [12]. Caspase inhibition and TNF neutralization assays BMDMs from BALB/c mice were treated with a pan-caspase-3/6/7 inhibitor (100 μM), caspase-3 inhibitor negative control (100 μM) (both from Calbiochem), anti murine TNF neutralizing antibody (5 μg/ml), isotype control antibody (5 μg/ml) (both from BD Bioscience), or pentoxifylline (Sigma, 100 μg/ml) for 1 h at 37°C/5% CO2 then infected with old M. smegmatis at MOI 10:1 for 2 h as described above. Cells

were then washed 3 times in PBS and incubated for an additional 20 h in DMEM infection media supplemented with the appropriate inhibitors and controls mentioned above and the apoptosis assay was performed. ROS detection assay Reactive oxygen species in BMDM and BMDD cells were detected at 2 h post infection using the ROS sensitive dye dihydroethidium (DHE) (Invitrogen). BMDM or BMDD cells were deprived of L929 supernatant or rGM-CSF respectively 16 hrs prior to infection and maintained in cytokine free media without phenol red for the length of the experiment. Post infection, cells were washed once in HBSS and then incubated in 2 μM DHE for 15 minutes. Cells were washed 3 times with HBSS, fixed with 4% paraformaldehyde and analyzed by flow cytometry.