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11 protocols using pam3csk4

1

Microglial responses to Borrelia burgdorferi

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Assays were carried out with approximately 1 to 2 × 104 cells/well of microglia seeded in 24-well tissue culture plates. At the time of the assay, the culture medium was removed and replaced with fresh medium without antibiotics, and the cells were pretreated with the pertinent inhibitors for 2 h prior to adding B. burgdorferi (MOI of 10:1). The microglial cells were incubated with the bacteria and inhibitors for a further 24 h, followed by collection of supernatant after centrifuging at 2,095 × g for 10 min at 4°C. Supernatants were stored at −20°C until analysis. The following inhibitors were used: SB203580 and BIRB796 (p38); U0126 (MEK1/2); SP600125 and Jun N-terminal kinase (JNK) inhibitor VIII (JNK) (all but one were from EMD Millipore, Billerica, MA; BIRB796 was obtained from Cayman Chemical Co., Ann Arbor, MI); and oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine (OxPAPC) (TLR2/4), CLI-095 (TLR4), Gefitinib (RipK2), and myeloid differentiation primary response 88 (MyD88) inhibitory peptide (InvivoGen, San Diego, CA).
Pam3CSK4 (Imgenex, San Diego, CA), LPS O55:B5 (Sigma-Aldrich, St. Louis, MO), or muramyl dipeptide (MDP, InvivoGen) were included as positive control agonists when required.
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2

TLR Signaling Stimulation Protocols

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For stimulation of TLR-signalling, cells were incubated with 5 ng/ml LPS from E.coli 0111:B4 (Sigmal-Aldrich, L2630), 10 μg/ml Poly IC (Invivogen, Tlrl-pic), 100 nM Pam3CSK4 (Imgenex, Img2201), 100 nM R848 (Alexis, ALX-420-038-M005) or 100 nM ODN1668 (Invivogen, tlrl-1668) in cell culture medium for indicated pre-treatment times. After pre-treatment, cells were carefully washed with medium 1x and subsequently used for infections or other experiments.
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3

Investigating Inflammatory Responses in Oligodendrocytes to Borrelia burgdorferi

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The role of TLRs in inducing inflammation in oligodendrocytes, in response to B. burgdorferi exposure was determined by gene silencing using small interfering RNA (siRNA) technology. Transfection complexes were generated using 2 μL HiPerfect transfection reagent (Qiagen, Valencia, CA) and 12.5–25 nM siRNA (Santa Cruz Biotechnology, Dallas, TX) in experimental medium. The complexes were incubated at room temperature for 30 min, and 200 μL of the complex was added to cells, after replacing the old medium in the 6-well plates. Immediately after the addition of transfection complexes, 800 μL of experimental medium was added to prevent drying of cell layer. After a 24-h incubation at 37 °C, 5% CO2, B. burgdorferi (MOI 10:1) was added and further incubated for 48 h, at the end of which, supernatants were collected as before and analyzed for chemokine and cytokine expression. A non-specific control siRNA was used as negative control for all experiments. Pam3CSK4 (Imgenex, San Diego, CA; TLR2), lipopolysaccharide (LPS) O55:B5 (Sigma Aldrich, St. Louis, MO; TLR4) were used as TLR-specific positive controls when required.
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4

Quantifying Endotoxin-Free MMP-2 Effects

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Purified endotoxin-free human and murine MMP-2 as well as its corresponding buffer (also referred as vehicle control in this manuscript) were purchased from Enzo/Biomol. MMP-2 was inactivated either by heating at 56°C for 45min or by pre-incubation with the MMP-2 inhibitor III at 100nM (Calbiochem) for 20min. rhMMP-9 and rmMMP-9 were purchased from Calbiochem and R&D Systems, respectively. rhGM-CSF and rhIL-4 were purchased from Immunex and R&D Systems, respectively. Pam3CSK4, MALP2 and Flagellin were from Imgenex. Zymosan and ultrapure LPS were from InvivoGen. Poly(I:C) was from Amersham. R848 was from 3M Pharmaceuticals. Inflammatory cytokines were quantified using CBA kits (BD Biosciences). The nuclear extraction as well as the TransAM NF-κB ELISA kits (Active Motif) were used according to the manufacturer’s instructions. The cell-permeable NEMO-binding domain inhibitory peptide (DRQIKIWFQNRRMKWKKTALDWSWLQTE) and its mutant (DRQIKIWFQNRRMKWKKTALDASALQTE) were from Calbiochem. Protein G-agarose (Pierce) was used according to the manufacturer’s instructions.
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5

Toll-Like Receptor Agonists Protocol

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Pam3CSK4 (TLR2 ligand; a synthetic triacylated lipopeptide) was purchased from Novus Biologicals (Littleton, CO, USA). LPS from S. minnesota (TLR4 ligand) was purchased from Wako Pure Chemical Industries (Osaka, Japan). Class B CpG-ODN (2007) (TLR21 ligand), (5′-TCGTCGTTGTCGTTTTGTCGTT-3′) was purchased from InvivoGen (San Diego, CA, USA). These regents were dissolved in sterile water and stored at −20°C until use.
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6

Murine Neuron Culture and RNA-seq

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phKCs (Lonza) were cultured in KBM‐Gold medium supplemented with KBM‐Gold SingleQuot KC (Lonza) for 3 days before use.10 Murine neurons were isolated from postnatal d5 C57BL/6 mice after deep anesthetization. The ganglia were digested and cultured in DMEM supplemented with 5% (v/v) FBS (Sigma), 100 U/ml penicillin, 100 μg/ml streptomycin, 1 × B27, and 50 ng/ml nerve growth factor (Sigma). Seven days of culture in the presence of 10 µM cytosine β‐d‐arabinofuranoside (Sigma) enriched >95% neurons characterized by NeuN staining. For RNA‐seq, neurons were incubated with a medium with either Pam3CSK4 (1 µg/ml, Novus), FSL‐1 (1 µg/ml, Sigma), Serpin E1 (20 µg/ml, Raybiotech), or the appropriate vehicle for 6 h.
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7

Extraction and Purification of Bacterial LPS

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In order to extract respective LPS from gastric bacteria, large-scale cultures of isolated strains were conducted in appropriate media as shown in Supplementary Table 3, Supplementary Digital Content 1, http://links.lww.com/CTG/A20. Five strains of each non-H. pylori bacterial cells and 3 strains of H. pylori cultured in broth and agar media were harvested by centrifugation (8,000 rpm, 15 minutes, 4 °C) or scraping of colonies. Approximately 170–220 mg LPS was extracted from the lyophilized bacterial cells (3–5 g dry weight) by a hot phenol–water method (26 ). In addition, purified LPS from H. pylori (GU2 and GC2) and Escherichia coli (E. coli) (2 lots of O55 and 2 lots of O111) were purchased from Wako Pure Chemicals (Tokyo, Japan). Crude LPS from Neisseria was treated with 10 μg/mL of DNase I (Takara Bio, Shiga, Tokyo), 10 μg/mL of RNase A (Sigma-Aldrich, MO), and proteinase K (Sigma-Aldrich) and purified by ultracentrifugation. Pam3CSK4, a TRL2 agonist, was purchased from Novus Bio (CO).
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8

Stimulation of Innate Immune Receptors

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Pam3CSK4 (TLR2 ligand; a synthetic triacylated lipopeptide), poly I:C (TLR3 ligand; a synthetic analog of doublestranded RNA), flagellin from S. typhimurium (TLR5 ligand), and imiquimod (R837; TLR7 ligand; an imidazoquinoline amine analog to guanosine) were purchased from Novus Biologicals (Littleton, CO, USA). LPS from S. minnesota (TLR4 ligand) was purchased from Wako Pure Chemical Industries, Ltd. (Osaka, Japan), and Class B CpG-ODN (2007) (TLR21 ligand) was purchased from InvivoGen (San Diego, CA, USA). The sequence of CpG-ODN was 5′-TCGTCGTTGTCGTTTTGTCGTT-3′. Stock solutions of Pam3CSK4 and poly I:C were prepared by dissolving them in sterile water (100 µg/mL and 100 mg/mL, respectively). LPS and flagellin were dissolved in phosphate-buffered saline (PBS) (1 mg/mL and 100 µg/mL, respectively), imiquimod was dissolved in dimethyl sulfoxide (DMSO) (100 mg/mL), and CpG-ODN was dissolved in water (10 mg/mL). BAY 11-7085 (NFκB inhibitor) was purchased from Abcam Co. (Cambridge, MA, USA), and was dissolved in DMSO at a concentration of 1 mM and stored at −20°C until use.
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9

Murine B Cell Stimulation Assay

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B cells were isolated from WT mouse spleens as described above and plated in 96-well plates at a density of 5 × 106 cells/ml in RPMI 1640 containing 5% fetal bovine serum, 1% L-glutamine, 200 μg/ml penicillin, 200 U/ml streptomycin (all from Corning). Cells were incubated overnight with one of four concentrations of LPS (1 μg/ml, 5 μg/ml, 10 μg/ml, 20 μg/ml), Pam3CSK4 (0.01 μg/ml, 0.05 μg/ml, 0.1 μg/ml, 0.2 μg/ml), flagellin (0.1 μg/ml, 0.5 μg/ml, 2 μg/ml, 10 μg/ml), MALP-2 (10 ng/ml, 50 ng/ml, 100 ng/ml, 200 ng/ml) (all from Novus Biologicals), recombinant mouse heat-shock protein 60 (HSP60) (0.5 μg/ml, 1 μg/ml, 5 μg/ml, 10 μg/ml) (Abcam), recombinant mouse high-mobility group protein B1 (HMGB1) (0.5 μg/ml, 2 μg/ml, 5 μg/ml, 20 μg/ml) (Biolegend), and low molecular weight hyaluronic acid (HA) (0.1 mg/ml, 0.2 mg/ml, 0.5 mg/ml, 1 mg/ml) (R&D Biosystems) (see Fig. 7). Control cells were maintained in RPMI media without stimulation. Cells were then incubated with 5 μg/ml brefeldin A (Biolegend) for 4 hours at 37°C, washed and stained for flow cytometry as described above. All experiments were run at least twice and included at least two technical replicates.
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10

Immunomodulatory Compounds for Cell Signaling

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Z-100 was produced by Zeria Pharmaceutical Co., Ltd. (Tokyo, Japan). Pam3CSK4 was purchased from Novus Biologicals (CO, U.S.A.). Muramyl dipeptide (MDP) and PG were purchased from InvivoGen (CA, U.S.A.). Spleen tyrosine kinase inhibitor IV (Syk inhibitor) was purchased from Merck (Darmstadt, Germany).
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