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113 protocols using ultrapure lps

1

Modulation of TLR Signaling by Acanthamoeba

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HCE cells were cultured in 24 well plates until confluent. Once confluent, cells were stimulated with or without A. castellanii (1×105 cells/ml) and Ultra-pure LPS (10 μg/ml) (InvivoGen, San Diego, CA, USA) for 24 hours. HEK-293 cells were exposed to A. castellanii in vitro. A. castellanii trophozoites (1×105/ml) were added to 24 well plates containing HEK-293 cells (1×106 cells/ml) for 24 hours. Cells cultured without the trophozoites served as a control. As a positive control, transfected HEK-293 cells were activated with 125 ng/ml poly (I:C) (polyinosinic:polycytidylic acid), a specific ligand for TLR3 (InvivoGen, San Diego, CA, USA); and 100 ng/ml ultrapure LPS, a specific ligand for TLR4/MD2 (InvivoGen, San Diego, CA, USA) for 24 hours as described previously [28] (link). HCORN cells were cultured in 24 well plates until confluent and then cells were stimulated with or without A. castellanii (1×105 cells/ml), A. culbertsoni (1×105 cells/ml), A. astronyxis (1×105 cells/ml), A. castellanii Neff (1×105 cells/ml) and Ultra-pure LPS (10 μg/ml) (InvivoGen, San Diego, CA, USA) for 24 hours.
Cells and supernatants were collected by centrifugation at 2000×g for 10 min at 4°C and analyzed for the expression of TLR1, TLR2, TLR3, TLR4, TLR9, IL-8, CXCL2 and GAPDH genes by RT-PCR. IL-8 and CXCL2 production in the supernatants was determined by ELISA.
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2

Inflammatory Signaling Pathway Analysis

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Standard LPS (E. coli 0111:B4, Cat No. tlrl-eblps), ultrapure LPS (E. coli 0111:B4, Cat No. tlrl-3pelps), nigericin (Cat No. tlrl-nig), ATP (Cat No. tlrl-atpl), and MSU (Cat No. tlrl-msu) were purchased from InvivoGen (San Diego, CA, United States); the cell lysis buffer (CLB) (Cat No. 9803) was bought from Cell Signaling Technology (Danvers, MA, United States); the mouse immunoglobin IgG protein (Cat No. ab198772) was purchased from Abcam (Cambridge, CB2 0AX, United Kingdom); Protein A/G PLUS-Agarose (Cat No. sc-2003) was obtained from Santa Cruz (Santa Cruz, CA, United States); mouse IL-1β (Cat No. 88–7013), tumor necrosis factor-α (TNF-α) (Cat No. 88-7324), interleukin-6 (IL-6) (Cat No. 88-701364), and a human IL-1β (Cat No. BMS22) ELISA kit was bought from Thermo Fisher (Waltham, MA United States); and the CellTiter-Glo® Luminescent Cell Viability Assay (Cat No. G7572) was from Promega.
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3

Autophagy and Inflammasome Activation Assays

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Antibodies used were: Flag (Sigma-Aldrich), HA (Roche), LC3 (Sigma-Aldrich), AMPK, ULK1 p-Ser 317, and p-Ser 555 (Cell Signaling Technology), NLRP1 (Cell Signaling Technology), NLRP3 (Adipogen), Caspase-1, and ULK1 (Santa Cruz Biotechnology, Inc.), and GFP, IRF3, Myc, and Actin (Abcam). To determine autophagic activity by immunoblotting, cells were cultured in the presence of bafilomycin A1, and lysates were subjected to immunoblotting as described previously (Mizushima et al., 2010 (link)). The reagents used were Ultrapure LPS (InvivoGen), IFN-γ (PeproTech), Cytotoxic LDH assay (Promega), and TO-PRO-3 Iodide (Life Technologies). Immunoblotting and immunostaining were conducted as previously described (Kyei et al., 2009 (link)). FAM-YVAD-FMK stainings (FLICA; ImmunoChemistry Technologies) were performed according to the manufacturer’s instructions.
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4

Cytokine Profiling of Mouse Bone Marrow-Derived Dendritic Cells

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Mouse bone marrow-derived dendritic cells (BM-DC) derived from naïve BALB/c mice (8 weeks of age; n = 3) were prepared as previously described [34 (link), 39 (link)]. Briefly, bone marrow precursors isolated from femurs and tibias were seeded at 2 x 105 cells/ml in RPMI 1640 culture medium containing 10% FCS, 150 μg/ml gentamycin, and 20 ng/ml mouse GM-CSF (Sigma-Aldrich, Germany) and incubated for 8 days. BM-DC (106 cells/well) were stimulated with formalin-inactivated B. longum strains Bl 7952 and Bl 372 (107 CFU/well), Pam3CSK4 (1 μg/ml), ultrapure LPS (1 μg/ml, InvivoGen, USA) or left untreated for 18 h. The levels of IL-10, IL-12p70, IL-6 and TNF-α were analysed in supernatants of stimulated cells by ELISA using Ready-Set-Go! kits (eBioscience, USA) according to manufacturer’s instructions. For cell surface marker analysis, BM-DC were labelled for 30 min at 4°C with anti-mouse FITC-conjugated CD11c, APC-conjugated MHC II and PE-conjugated CD40, CD80 or CD86 monoclonal antibodies (eBioscience, USA). The data were acquired on a BD FACSAria III flow cytometer (BD Biosciences, USA) and analysed with FlowJo software 7.6.2 (TreeStar, USA).
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5

Immune Cell Activation Signaling Assays

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The study was approved by the joint University College London/University College London Hospitals National Health Service Trust Human Research Ethics Committee (ref. 10/H0720/14). The PBMCs were obtained by venepuncture of healthy volunteers and density‐gradient centrifugation. Monocyte‐derived dendritic cells (MDDC) were derived from magnetically sorted CD14‐positive monocytes differentiated in RPMI‐1640 culture media (Sigma, St Louis, MO) with 10% fetal calf serum, 100 ng/ml granulocyte–macrophage colony‐stimulating factor (GM‐CSF) and 50 ng/ml IL‐4 for 4 days.2 Monocyte‐derived macrophages (MDM) were derived after adherence to tissue‐culture plastic and culture for 6 days in RPMI‐1640 with 10% autologous serum and 20 ng/ml macrophage colony‐stimulating factor (M‐CSF).2 The PBMC, MDDC and MDM were stimulated with either 100 ng/ml ultrapure LPS (Invivogen, San Diego, CA) as Toll‐like receptor 4 (TLR4) ligand, or with 1 μg/ml Pam2CSK4 (PCSK, Invivogen) as a TLR2 ligand for 30 min to measure phosphorylation of p38 and NF‐κB p65 by flow cytometry, 60 min to undertake quantitative confocal microscopy to evaluate nuclear translocation of NF‐κB p65, and 4 hr to measure transcriptional responses.
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6

Quantification of Inflammatory Cytokines

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Ultrapure LPS was obtained from InvivoGen, nigericin was obtained from Invitrogen, okadaic acid was obtained from Calbiochem, lethal factor and protective antigen were obtained from List Biological Laboratories, and Gene Juice was purchased from Merck. DRAQ5 was purchased from eBioscience. The ELISA kits for mouse IL-1β and mouse TNF were obtained from R&D Systems and were used according to the manufacturer’s instructions.
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7

Bone Marrow Dendritic Cell Stimulation

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Bone marrow derived dendritic cells (BMDC) were cultured from C57BL/6 bone marrow in RPMI/20% FBS supplemented with GM-CSF and IL-4 as described70 (link). After 7 days the non-adherent cells were harvested and split into two aliquots, one of which was stimulated for 3 hours with 102 Eu/ml Ultrapure LPS (Invivogen) at 37°C. EL4 cells, and HPV16 E7-expressing EL4 cells generated as described71 (link), were cultured in RPMI/20% FBS. Cell pellets were analysed by Real-Time PCR as described below.
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8

Monocyte Cytokine Modulation Assay

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CD14+ cells were isolated from PBMC by positive selection using CD14 human microbeads (Miltenyi Biotec) according to manufacturer’s instructions. The cells were cultured (5 × 105 cells/mL) in DMEM L-Glutamine medium containing 10% heat-inactivated fetal calf serum and supplemented with 50 µM 2-Mercaptoethanol and 250 µM recombinant human IL-2 using flat-bottom 96-well suspension plates. Cells were stimulated with 1 ng/ml ultrapure LPS (Invivogen, San Diego, CA, USA) in the presence or absence of conditioned media (1:50 dilution) from T cells cultured with CD3/CD28 +/− DLL4/STAT3 cytokines. Anti-IL10R blocking antibody (clone 3F9) was added where indicated (1 µg/ml). After 7 h, cells were collected and gene expression was analysed via Real-Time PCR.
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9

Immune Cell Activation Assay

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Ultrapure LPS, flagellin, nigericin, CpG oligonucleotide, and poly(dA:dT) were purchased from InvivoGen. Silica (MIN-U-SIL 15) was obtained from US Silica. ATP was from Sigma-Aldrich. Pam3Cys was from EMC Microcollections. X-tremeGENE HP DNA transfection reagent was from Roche. Transfection reagent Profect P1 was from Targeting Systems. Acridine Orange (L13159) was from Alfa Aesar. TRIzol reagent (15596018), BAPTA-AM (B1205), and Alexa Fluor 594-labeled zymosan particles (Z23374) were from Thermo Fisher Scientific. Antibodies for immunoblotting include anti-CHMP4B (13683-1-AP) from Proteintech; anti-IKKα (05-536) from Millipore; anti-Mcu (14997), anti-phospho-IkBα (S32), anti-phospho-IKKα/β (S176/180), anti-phospho-p65(S536), anti-p65, anti-phospho-ERK1/2 (T202/Y204), anti-phospho-JNK (T183/Y185), and anti-phospho-p38 (T180/Y182) from Cell Signaling Technology; anti-β-actin (sc-1615) from Santa Cruz Biotechnology; anti-NLRP3 (Cryo-2), anti-Asc (AL177), and anti-caspase-1 (AG-20B-0042) from Adipogen; and anti-IL-1β (AF-401-NA) from R&D Systems. Antibodies for the flow cytometry assay include anti-CD45-PE Cy7 (103114), anti-CD11b-FITC (101206), anti-Ly-6G-PB (127612), and anti-Ly-6C-PE (128008) from BioLegend.
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10

Monocyte-derived dendritic cell response to polymer nanocomposites

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Resting human monocyte-derived dendritic cells (moDCs) were cultured for 24 hours on the surface of the prepared, sterilized by UV light, polymer nanocomposites in the presence or absence of the specific Toll-like receptor (TLR) ligand bacterial lipopolysaccharide (LPS) (250 ng/mL ultrapure LPS, InvivoGen, San Diego, CA, USA) for 24 hours. As human moDCs are highly sensitive for LPS the reagents and lab equipment are endotoxin-free. Some samples were cultured with both – polymer nanocomposites and LPS (nanocomposites + LPS) to detect the effect of nanocomposites on moDC viability and activation under microbial stimuli of LPS, while untreated cells (ctrl) were served as negative controls.
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