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9 protocols using ir680

1

Western Blot Analysis of TRPM7, MycN, and ODC

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Cell lysates were prepared in RIPA buffer [20 mM Tris–HCl, pH 7.5, 0.1% (w/v) sodium lauryl sulfate, 0.5% (w/v) sodium deoxycholate, 135 mM NaCl, 1% (v/v) Triton X-100, 10% (v/v) glycerol, 2 mM EDTA], supplemented with Complete protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN, USA), and phosphatase inhibitors sodium fluoride (NaF) (20 mM) and sodium vanadate (Na3VO4) (0.27 mM). Western blot analysis was performed as previously described [28] (link). The total protein concentration was determined using the protein assay dye reagent from Bio-Rad Laboratories (Hercules, CA, USA). Cell lysates in SDS-sample buffer were boiled for 5 min and equal amounts of total protein analyzed by 10% SDS–polyacrylamide gel electrophoresis (SDS–PAGE) and western blotting. The antibodies used in this study are: rabbit monoclonal TRPM7 (at a 1:1000 dilution from Epitomics, Inc. (Burlingame, CA, USA)), rabbit polyclonal MycN (at a 1:500 dilution), goat polyclonal ODC (at a 1:500 dilution) and mouse monoclonal GADPH (at a 1:1000 dilution) (Santa Cruz Biotechnology, Santa Cruz, CA, USA). Secondary anti-mouse (at a 1:10,000 dilution) IR-680 or IR-800 (LI-COR Biosciences, Lincoln, NB, USA). Proteins were detected using the Odyssey Infrared Imaging System (LI-COR Biosciences, Lincoln, NB, USA) and analyzed with Licor Image Studio 2.0 acquisition and analysis software.
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2

Immunoblotting Procedure for Protein Expression

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Immunoblotting was performed as described (60 (link)). Briefly, cultured cells were lysed using radioimmunoprecipitation assay buffer supplemented with a protease inhibitor cocktail (Roche). Proteins were resolved with SDS–polyacrylamide gel electrophoresis, and after transfer to a nitrocellulose membrane were blocked in Odyssey blocking buffer (LI-COR). The following primary antibodies were used: human NAF1 (rabbit, ab157106, 1:1000; Abcam), mouse Naf1 (rabbit, Naf1 394, 1:250; Prosci), Myc (mouse, clone 4A6, 1:1000; Millipore), human dyskerin (rabbit, sc-48794, 1:250; Santa Cruz Biotechnology), and green fluorescent protein (mouse, 7.1 and 13.1, 1:1000; Roche) with loading controls actin (mouse, ab8226, 1:2000; Abcam), tubulin (rabbit, ab6046, 1:5000; Abcam), PARP (rabbit, 9542S, 1:1000; Cell Signaling Technology), or GAPDH (mouse, mAbcam9498, 1:1000; Abcam). Secondary antibodies were conjugated to dyes IR680 or IR800 (donkey, 1:10,000; LI-COR), and blots were visualized using an Odyssey scanner (LI-COR), with exception of the mouse Naf1 antibody that was visualized by horseradish peroxidase–linked antibody (rabbit, 7074, 1:10,000; Cell Signaling Technology) and enhanced chemiluminescent substrate (Thermo Scientific). Cell fractionation was performed using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Scientific).
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3

Cell Lysis and Protein Analysis

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For protein analysis, cleared NP40 lysates and whole cell SDS lysates were prepared from 10-cm dishes containing cells at 100% confluency as described [17 (link), 26 (link)]. Protein concentration was measured by BCA assay and 50 micrograms protein was loaded per lane. Immunoprecipitations were performed as described except that the buffer contained 0.5% NP40 [11 (link)]. Antibodies for E-cadherin, N-cadherin, beta catenin, phospho-beta catenin, beta four integrin, and fibronectin were all rabbit polyclonal from Cell Signaling; for Myc-tag (clone 9E10.3), from Neomarkers; for FLAG tag (clone M2), Agilent; for actin (125-ACT), from PhosphoSolutions; for GFP, from Abcam; for vimentin, from Millipore. ZO-1 antibody was from PTG. The CLCA2 antibody TVE20 has been described (12). The protein size marker was Dual color (Bio-Rad). Secondary antibodies were labeled with IR680 or IR800 (Licor), and protein expression was quantified on an Odyssey instrument (Licor).
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4

Immunoblotting of Stress Response Proteins

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Blue lysis samples were thawed and boiled for 5 min with the addition of 10% BME. Lysates were then loaded on a 4–12% Bis-Tris Protein mini gel (1.0 mm; Life Technologies) and the separated proteins were transferred to a polyvinylidene difluoride (PVDF) membrane. After blocking in Odyssey TBS buffer (Li-COR) blots were incubated overnight at 4°C with primary antibodies against total p38MAPK (Cell Signaling), p38 MAPK T180/Y182 (Cell Signaling), COX IV (Li-Cor), total HSP 27 (Cell Signaling), HSP27 S82 (Cell Signaling), and GAPDH (Santa Cruz). The bound primary antibody was then detected with the appropriate secondary antibodies, IR680 or IR800 conjugated goat anti-mouse or goat anti-rabbit IgG (Li-COR). Blots were imaged on the Li-COR Odyssey CLx and images were analyzed utilizing Li-COR Image Studio Ver 5.2 software. The data was analyzed by two-way ANOVA for multiple comparisons in GraphPad Prism.
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5

Western Blot Analysis of p53

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Cells were harvested by lysis in the presence of protease inhibitors, and run on 4–12% Bis-Tris gradient gel (Invitrogen). Protein was transferred onto Nitrocellulose membrane and the membrane was blocked with 5% nonfat dried milk prior to antibody addition. p53 (1:3000, DO1 Santa Cruz), Actin (1:10000, Sigma) antibodies were used. Secondary antibodies with IR-680 (1:10000, Licor) were used for detection.
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6

Western Blot Analysis of MtlA and MtlR

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Bacteria were grown to an OD600 ~0.3 and collected (8000 g, 5 min). For MtlA analysis, lysates were prepared by mixing ~107 cells with SDS-loading buffer and heating at 95 °C for 10 min. For MtlR analysis, cell pellets from 5 to 50 ml cultures were lysed with B-PER Extraction Reagent (Thermo Fisher Scientific) in the presence of DNAse I, following the suggested protocol of the manufacturer; the lysate was then mixed with SDS-loading buffer. The proteins were resolved on 4–20 % TRIS gels (Bio-Rad) and transferred to nitrocellulose membranes. The membranes were treated with polyclonal anti-FLAG (abCam), polyclonal anti-HA (abCam), monoclonal anti-RpoB (abCam), or monoclonal anti-RNAPα (BioLegend) antibodies. Antibodies were detected using secondary antibodies with IR680 and IR800 dyes attached (Licor). As a membrane protein, MtlA has a tendency to oligomerize, even under the denaturing conditions of SDS-PAGE. Signals were visualized and band densities were measured using an Odyssey imager (Licor).
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7

Western Blot Analysis of Cell Lysates

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Cells were harvested by lysis in the presence of protease inhibitors, and run on 4%–12% Bis-Tris gradient gel (Invitrogen). Transfer was done onto Nitrocellulose membrane and the membrane was blocked with 5% nonfat dried milk prior to antibody addition. p21 (1:1 000, Calbiochem), p53 (1:8 000, DO1 Santa Cruz), Actin (1:10 000, Sigma) and RFP (1:5 000, MBL) antibodies were used. Secondary antibodies with IR-680, IR-800 dyes (1:10 000, Licor) were used for detection.
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8

4-HNE Protein Adducts Analysis

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Protein from frozen striatum and midbrain was extracted with 1 × radioimmunoprecipitation assay buffer (CST, Beverly, MA, USA) with 1 × Calbiochem Protease Inhibitor Cocktail Set I and 1 × Halt* Phosphatase Inhibitor Cocktail (Thermo Scientific). A Tissue Lyser LT (Invitrogen, Pleasanton, CA, USA) with a 5 mm steel bead was used to homogenize tissues at 50 Hz. Tissue lysate was then centrifuged at 13,000 rpm for 15 min at 4°C. Supernatant was saved in a –80°C freezer. Bradford protein assay reagents (Bio-Rad, Irvine, CA, USA) were used to determine protein concentration. Protein (40 μg/lane) was then separated on a 4–12% Criterion sodium dodecyl sulfate–polyacrylamide gel electrophoresis gel (Bio-Rad) and transferred on to nitrocellulose membrane. Proteins were detected with antibodies directed specifically to 4-HNE protein adducts (R&D, Minneapolis, MN, USA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (CST), respectively, in the midbrain and striatum of 6- and 18-month-old mice. An appropriate secondary antibody from LiCor (IR800 or IR680) was used corresponding to each primary antibody. Immunoreactive bands were imaged and quantified using Odyssey software (LiCor, Lincoln, NE, USA).
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9

Quantifying VASP Phosphorylation in ASM Cells

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Following previously detailed protocols [32 ,39 (link)], ASM cells were seeded in 96-well plates (5,000 cells/well) overnight and treated with VEH or BAY60 (0.1–10 µM) for desired time points. Cells were immunolabeled using rabbit anti-VASP.S239 (1:500; Cell Signaling) or mouse anti α-tubulin (1:500; Sigma) primary antibodies, then labeled using near infrared secondary antibodies (IR680 and IR800; LiCor). Proteins were quantified by scanning well fluorescence on the IR Odyssey® Imager (CLx, LI-COR Biosciences, Lincoln, NE) and normalized with respect to α-tubulin content.
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