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8 protocols using birb796

1

Isolation and Culture of LGR5+ Lung Fibroblasts

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For LGR5+ fibroblasts cultures, human intralobar airways were micro dissected, and the distal region was cut out to enrich airways measuring 1–2 mm in their outer diameter and contiguous alveoli. Dissected tissue was dissociated using protease mix (4 mg/ml pronase, 5 U/ml dispase, 1 mg/ml collagenease type IV, and 0.33 U/ml DNase I, Collagenase type I) as described above in section (Human lung microdissection, tissue dissociation and scRNA-seq). Dissociated cell suspension was cultured in LGR5 fibroblast enrichment medium containing base medium along with 3 μM CHIR99021 (Cayman, #13122), 1 μM BIRB796 (Tocris, #5989), 50 ng/ml human EGF (Gibco, #PHG0313), 10ng/ml PDGFRα, 10ng/ml Noggin, and 10ng/ml FGF10 (BioLegend, #559306). After initial passage, mesenchymal cells were isolated by depleting the epithelial cells using EpCAM magnetic beads.
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2

Inflammatory Signaling Regulation Protocol

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LPS (Lipopolysaccharide Escherichia coli serotype O111:B4, #LPS25), anisomycin (#A5862), rapamycin (#553211), MG-132 (#474791) and cycloheximide (#C-0943) were purchased from Sigma, BIRB796 (#5989) and Torin1 (#4247) from Tocris.
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3

Investigating Apoptosis Signaling Pathways

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LicA (BP0855) was purchased from Chengdu Biopurify Phytochemicals Ltd. (Chengdu, China). Primary antibodies against p-ERK, cleaved caspase-3, cleaved caspase-9, and cleaved poly (ADP-ribose) polymerase (PARP) were bought from Cell Signaling Technologies (Beverly, MA, USA). Primary antibodies against Bcl-2, Mcl-1, Bax, t-ERK, p-p38, t-p38, p-JNK, t-JNK, β-actin, and siRNA-p38 (sip38) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Moreover, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) was purchased from Sigma-Aldrich (St. Louis, MO, USA). Z-VAD-FMK and tauroursodeoxycholic acid (TUDCA) were purchased from BioVision (Milpitas, CA, USA). BIRB 796 was bought from Tocris Bioscience (Minneapolis, MN, USA). Fetal bovine serum (FBS) was purchased from HyClone (Logan, UT, USA).
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4

Modulating p38 Pathway Impacts ASFV Replication

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To assess the impact of activation or inhibition of p38 on ASFV replication, 1.5 × 106 moMΦ per sample were infected with an MOI of 1 either in the presence of conditioned medium or the p38-inhibitor BIRB796 (25 nM in DMSO, Tocris), or after a 4 h pretreatment with the p38-activator TNFα (20 ng/mL in 5% trehalose, Biolegend). The conditioned medium was prepared by three sequential filtrations of the virus stock through 0.1 µm sterile syringe filters (qpore). At 6 and 24 hpi moMΦ lysates were prepared and the expression and phosphorylation of MAPK14/p38 was assessed by immunoblotting. Supernatants for the determination of virus titers were collected at 24 hpi.
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5

Inhibition of A. phagocytophilum Infection

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Stock (10 mM) of BIRB796 (Tocris, USA) was made in dimethyl sulfoxide (DMSO) solution. The stock solution was diluted with tick cell media to a final concentration of 10 μM. Mock solution was prepared in a similar way but without BIRB796. Tick cells (1 × 105) were seeded onto 12 well plates and incubated for 16–20 h. Following incubation, tick cells were treated with 10 μM BIRB796 for 4 h followed by A. phagocytophilum (isolated from 2 × 105 NCH-1 infected HL-60 cells) infection. Equal volumes of mock solution (corresponding to 10 μM volume) was added to control cells. The cells were then incubated for 24 h and processed further for RNA and protein extractions to measure p38 mapk transcripts and protein levels, respectively. In other experiments, after 16–20 h post plating, tick cells were treated with 100 μM XA and 20 μM BIRB796 for 4 h followed by A. phagocytophilum infection. Equal volume of mock solutions (corresponding to 100 μM XA and 20 μM BIRB796 vol) were added to control cells. The cells were incubated for 24 h and processed for DNA extractions to measure bacterial loads.
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6

Endothelial Cell Activation Assay

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KT5720 (PKA inhibitor), PKI 14–22 amide, p53 inhibitors (Pifithrin α and µ), p38 MAP kinases inhibitors (BIRB796 and SB202190), Sphingosine-1-P, Forskolin, and the NF-κB inhibitor BAY11-7085 were all purchased from Tocris (Bristol, UK). For immunostainings, Phalloidin 547 (FP-AZ0330) was from FluoProbes, Interchim, (Montluçon, France), while the FITC-conjugated mouse anti-VE-Cadherin (CD144) antibody (clone 55-7H1, cat no. 580411) was from BD Pharmingen (Franklin Lakes, NJ, USA). The mounting medium (DAPI Fluoromount-GTM (cat no. 0100-20)) was purchased from Southern Biotech (Birmingham, AL, USA). For flow cytometry analysis, all antibodies (BB515 mouse anti-human CD54 (ICAM-1, cat no. 564685), BUV737 mouse anti-human CD106 (VCAM-1, cat no. 565418), PE mouse anti-human CD62P (P-Selectin, cat no. 555524), APC mouse anti-human CD62E (E-Selectin, cat no. 551144)), and the FITC Annexin V/Propidium Iodide apoptosis detection kit were obtained from BD Biosciences (Franklin Lakes, NJ, USA).
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7

Cytokine and Inhibitor Preparation Protocol

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Recombinant human IL1β (R&D Systems) and TNF-α (R&D Systems) were dissolved in PBS containing 0.1% bovine serum albumin (Sigma-Aldrich). Budesonide (gift from AstraZeneca), dexamethasone (Sigma-Aldrich), SB203580 (Calbiochem), JNK-IN-VIII (Calbiochem), U0126 (Calbiochem), BIRB796 (Tocris), and VX745 (Tocris) were dissolved in dimethyl sulfoxide as stocks of 10 μM. Toll-like receptor 2 agonists, Pam2CSK4, and Pam3CSK4 (both Invivogen) were prepared as stocks of 1 mg/ml in sterile water.
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8

Recombinant Growth Factor Acquisition

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Recombinant human vascular endothelial growth factor (VEGF)-A165 was purchased from R&D Systems Inc. (Abingdon, UK). Recombinant human epidermal growth factor (EGF) was purchased from Peprotech (London, UK). BIX02189, AX15836 and BIRB796 were purchased from Tocris Bioscience (Bristol, UK), and JWG071 was purchased from Sigma (Poole, UK).
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