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6 protocols using ephb4

1

Immunoblotting of Retinal Proteins

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For immunoblotting, freshly isolated P5 retina or cells were lysed in Cell Lysis Buffer (Cell Signaling Technology, #9803) and protein concentrations determined. Protein samples were resolved by SDS-PAGE, transferred to nitrocellulose membranes, and incubated with appropriate primary antibodies. After incubating with fluorescence-conjugated secondary antibodies, immunoreactive proteins were visualized by an Odyssey infrared imaging system (LI-COR Biotechnology, Nebraska). Densitometric analysis of the blots was performed with Odyssey software (LI-COR Biotechnology). Results were normalized by arbitrarily setting the densitometry of control samples to 1.0. The antibodies used were GIT1 (Santa Cruz, sc-9657), Notch1 (EMD Millipore 07-220), Dll4 (Santa Cruz, sc-28915), VEGFR3 (eBiosciences, 16-5988-81), VE-cadherin (Santa Cruz, sc-6458), Flt-1 (Santa Cruz, sc-316), EphrinB2 (Santa Cruz, sc-1010), EphB4 (Santa Cruz, sc-5536), Hey1 (Millipore, AB5714) and RBP-J (Santa Cruz, sc-28713). IP was performed as published previously(Pang et al., 2008 ).
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2

Tracheal Endothelial Cell Isolation and Manipulation

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As previously reported, tracheal segments devoid of large veins from C57BL/6 mice were dissected, minced and digested [9] (link). The cellular digest was filtered and centrifuged, the cell pellet was resuspended and placed on a gelatin-coated 35 mm dish. After 5–7 days, cells positively labeled with fluorescent Dil-ac-LDL (Molecular Probes, Eugene, OR) as an endothelial cell marker and labeled EphB4 (Santa-Cruz, Santa Cruz, CA) as a marker of venous endothelial cells were selected using the FACSAria cell-sorting system (BD Biosciences, San Jose, CA) and replated (0.2% gelatin-coated T-25 flask). Depending on outcome variable and prior to challenge, TvEC were incubated (2% FBS DMEM; 2 h) and treated with vehicle, NG-nitro-L-arginine methyl ester (L-NAME; 10−5 M), N-acetylcysteine amide (NACA; 5×10−3 M), superoxide dismutase (SOD; 10−5 M) or excess BH4 (10−4 M [17] for 30 min prior to challenge, TvEC were distended with the Flexercell tension Plus System (FX-4000T; Flexcell Int, Hillsborough, NC) using 5% elongation representing physiological levels of ventilatory stretch, 18% elongation representing pathophysiological overdistension [9] (link), [18] or treated with thrombin (5 Units/ml) all for 5 min exposures.
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3

Andrographolide-Induced Apoptosis and Autophagy

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Andrographolide (purity > 98%) was purchased from the National Institutes for Food and Drug Control, China. Arsenic trioxide (As2O3), trypsin, phosphate buffer saline (PBS), ethylene diamine tetraacetic acid (EDTA), 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide (MTT), monodansylcadaverine (MDC), propidium iodide (PI), Annexin V, and rapamycin were purchased from Sigma Chemical Corp. (St. Louis, MO, USA). Primary antibodies against caspase-3, LC3, Atg-5, EphB4 and VEGFR1 were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). All the other chemical reagents in the study were of analytical reagent grade.
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4

Analyzing EPHB2, EPHB4, and EPZH2 in Cell Lines

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Whole cell extracts of cell lines were used in Western blots for EPHB2 (Santa Cruz, Dallas, TX, USA, #sc-130752), EPHB4 (Santa Cruz, #sc-5536), and GAPDH (Santa Cruz, #sc-51631). Nuclear extracts for Co-IP were prepared and diluted using the NE-PER Nuclear and Cytoplasmic Extraction Kit (Thermo Fisher Scientific, #78835) and RIPA buffer (Life Technologies, Grand Island, NY, USA, 89900). The IP was incubated with JMJD3 antibody (Abcam, #ab38113), Notch intracellular domain (NICD) antibody (Abcam, # ab8925), or EZH2 antibody (Abcam, #ab186006) overnight at 4°C, the protein G Dyna-beads (Life Technologies, 10009D) were added and incubated at 4°C for 3 hours. After washing with RIPA buffer three times, the beads were resuspended in reducing SDS gel loading buffer. The gray-scale assay for each blots was analyzed using MultiGauge V3.0 software (Fujifilm, Tokyo, Japan), and number under each blots presents the relative level compared with the vector or Scrss.
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5

Immunohistochemical Analysis of Ephrin and Eph Receptors

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Tibias were fixed with 4% paraformaldehyde in PBS (4% PFA/PBS) overnight at 4 C, embedded in paraffin, and cut into 5 µm sections. The sections were stained by immunohistochemisty for ephrin B2 (sc-15397, Santa Cruz Biotechnology, Inc., Santa Cruz, CA), Eph B4 (sc-5536, Santa Cruz Biotechnology, Inc., Santa Cruz, CA), and counterstained with hematoxylin.
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6

Protein Extraction and Western Blot

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Total protein extraction and Western blot were performed as described previously (12 (link), 35 (link)). The following antibodies were used: PDCD10 (1:400; Atlas Antibodies); EphB4 (1:400, Santa Cruz), p-Erk1/2, p-Akt, and GAPDH (each 1:1000 dilution, Cell Signaling Technology).
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