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3 protocols using gentamicin

1

MAIT Cell Activation by Salmonella

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PBMCs were seeded in 96-well round-bottom plates (5 to 8 × 105 cells per well) and infected with the different Salmonella strains from frozen midlog phase stocks, at the indicated MOI. Upon 80-min incubation at 37 °C, 100 μg/mL gentamicin (Lonza) was added to kill extracellular bacteria. A total of 200 μg/mL of gentamicin was required for the experiments carried out in Malawi using ST313 strains from lineages 1 and 2.
At 180 min postinfection, 5 ng/mL brefeldin A (BioLegend) solution was added to every well in order to achieve accumulation of intracellular cytokines. Samples were incubated overnight at 37 °C for no more than 15 h.
For MR1 blocking experiments, infection was performed in the presence of 30 μg/mL MR1 blocking antibody 26.5 (42 (link)) or mouse IgG2a isotype control (ATCC). The MAIT agonists 5-A-RU was synthesized as described in ref. 71 (link) and 1 μg/mL was combined to 50 μM MG (Sigma).
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2

Murine Macrophage Differentiation Protocol

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Bone marrow was collected from 12- to 16-week-old female wild-type C57BL/6 mice (experiments approved by the animal experiments committee of the Academic Medical Center, Amsterdam) and cultured in 100 mm cell culture dishes (BD Falcon) in IMDM (Lonza) supplemented with 10% FBS, 86 μg ml−1 gentamicin and 40 ng ml−1 recombinant mouse M-CSF (Biolegend). At day 3, fresh medium containing M-CSF was added. At day 6, M-CSF and either 10 ng ml−1 recombinant mouse IL-10 or 20 ng ml−1 recombinant mouse IL-4 (both from eBioscience) were added. At day 7, cells were harvested and stimulated as described for human macrophages, using 2 μg ml−1 mouse IgG (Equitech-Bio) coated in Maxisorp plates. Cells were analysed by quantitative RT–PCR as described; primer pairs are listed in Supplementary Table 2.
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3

Cytokine Production by AIEC-infected MoDCs

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MoDC were obtained from CD14+ human monocytes purified from blood of healthy subjects as previously described.30 (link) MoDCs were seeded into round-bottom, 96-well culture plates at a density of 105 cells/well in complete RPMI medium without penicillin/streptomycin and infected with 107 CFU/mL of AIEC-LF82 or E. coli Nissle 1917 strain alone [MOI 10:1 bacteria per phagocytic cell]. Following 1 h of phagocytosis, gentamicin [20 ug/mL, Sigma-Aldrich, Darmstadt, Germany] was added to kill extracellular bacteria. Subsequently, infected MoDC were washed and maintained in RPMI supplemented with gentamicin [2 ug/mL] for additional 22 h. The levels of IL-1β [BioLegend], IL-12p70 [BioLegend], IL-23p19 [R&D Systems], IL-6 [ImmunoTools], IP-10 [R&D Systems], and RANTES [R&D Systems] in supernatants of infected MoDC were analysed after 24 h by ELISA. The ELISA plates were read on a microplate reader [SAFAS MP96], and data were analysed with Prism software [version 7; GraphPad Software, La Jolla, CA].
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