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112 protocols using anti ha

1

Immunoprecipitation of Schistosoma Proteins

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Immunoprecipitation of SmHDAC8, SmDia-RBD and SmRho1 (isoforms and mutant constructs) proteins expressed in oocytes was performed using HA and Myc tags respectively. 15h after cRNA injection in the equatorial region, oocytes were lysed in buffer (50 mM HEPES pH 7.4, 500 mM NaCl, 0.05% SDS, 0.5% Triton X100, 5 mM MgCl2, 1 mg mL-1 bovine serum albumin, 10 mg mL-1 leupeptin, 10 mg mL-1 aprotinin, 10 mg mL-1 soybean trypsin inhibitor, 10 mg mL-1 benzamidine, 1 mM sodium vanadate) and centrifuged at 4°C for 15 min at 10 000 x G. Supernatants were incubated with anti-Myc (1/100; Invitrogen) and anti-HA (1/100 Invitrogen) antibodies for 4 h at 4°C. Protein A-Sepharose beads (5 mg, Amersham Biosciences) were added for 1 h at 4°C. Immune complexes were collected by centrifugation, rinsed three times, resuspended in Laemmli sample buffer, and subjected to a 10% SDS-PAGE. Immune complexes were analyzed by Western Blotting using anti-Myc (1/50 000, Sigma Aldrich) or anti-HA (1/10 000, Invitrogen) antibodies and the advanced ECL detection system (Amersham Biosciences).
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2

Antibody Detection of Epitope-Tagged Proteins

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The HA epitope was detected with mouse monoclonal antibody (mAb) HA.11 (BioLegend; 901515) and rabbit polyclonal antibody (pAb) anti-HA (Invitrogen; PI715500). The Ty1 epitope was detected with mouse mAb BB2 [61 (link)]. The c-Myc epitope was detected with mouse mAb 9E10 [62 (link)]. The V5 epitope was detected with mouse mAb anti-V5 (Invitrogen; R96025) and rabbit mAb anti-V5 (Cell Signaling Technology; 13202S). The OLLAS epitope was detected with rat mAb anti-OLLAS [63 (link)]. Toxoplasma-specific antibodies include rabbit pAb anti-IMC6 [64 (link)], mouse mAb anti-IMC1 [65 (link)], mouse mAb anti-ISP1 [32 (link)], rabbit pAb anti-Centrin1 (Kerafast; EBC004) [66 (link)], and rabbit anti-Catalase [67 (link)].
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3

Purification and Analysis of RSPO2 Variants

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Recombinant full-length human RSPO2 was purchased from R&D Systems. RSPO2-Fu-WT and RSPO2-Fu-F109A were purified as described previously25 (link). For western blot analysis, anti-HA (Invitrogen cat #71–5500), anti-FLAG (Sigma cat # F7425), anti-β-actin (Cell Signaling cat #4970), anti-β-catenin (Cell Signaling cat #9562), anti-Axin1 (Cell Signaling cat #2087), anti-Axin2 (Cell Signaling cat #2151), anti-phosphor-ERK (Cell Signaling cat #9101), total ERK (Cell Signaling cat #4695), anti-PARP (cell signaling cat #9532), and anti-GAPDH (Cell Signaling cat #2118) were used. For ICC, anti-HA-Alexa 488 (Cell Signaling cat #2350), anti-human-Alexa 488 or –Alexa 555 (Invitrogen cat #A11013 and #A21433) were used. For western blotting, cells were lysed with RIPA buffer (50 mM Tris-Cl pH 7.4, 150 mM NaCl, 1 mM DTT, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS), supplemented with protease and phosphatase inhibitors, and reduced at 37 °C for 1 hr. HRP-conjugated secondary rabbit or mouse antibodies (Cell Signaling) were used following the standard ECL protocol. For cytoplasmic β-catenin analysis, whole cell lysates were incubated with agarose bound concanavalin A beads to remove membrane-bound β-catenin and the remaining fractions were used as previously described40 (link).
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4

Western Blot Analysis of B. glumae Proteins

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Total lysates from the B. glumae and E. coli strains were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene fluoride (PVDF) membranes. The membranes were blocked using 4% skim milk and incubated with anti-ObcA (1:4000) plus anti-ObcB (1:3000), anti-TofR (1:3000), anti-HA (Invitrogen, 1:2500), and anti-His (Invitrogen, 1:3000) antibodies. Proteins were detected using a secondary anti-rabbit horseradish peroxidase-conjugated IgG antibody (Cell Signaling), a secondary anti-mouse horseradish peroxidase-conjugated IgG antibody (Cell Signaling), and a chemiluminescent substrate (Bio-Rad). Antibodies against B. glumae ObcA, ObcB, Lon, and TofR were generated in rabbits immunized with ObcA-6xHis, a peptide of ObcB (N-GNIEFYADQRRPQYLRELVRVTR-C), a peptide of Lon (N-GLPWRKKSKVNNDLSNAE-C), and TofR-6xHis. The density (pixels/inch) of each band was measured using ImageJ version 1.53a software (NIH). All experiments were performed using three independent replicates.
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5

Western Blot Analysis of Membrane Proteins

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Pulldowns samples were eluted, boiled in Laemmli buffer and resolved by SDS-PAGE in 7%, 12% or 15% acrylamide-bisacrylamide gels or in Mini-PROTEAN TGX Gels (Bio-Rad) then, the gels were then transferred to a nitrocellulose membrane (Bio-Rad) using the Trans-Blot Turbo Transfect Pack (Bio-Rad) and the Trans-Blot Turbo system (Bio-Rad) and detected with the corresponding antibodies anti-GFP (Santa Cruz Biotechnology), anti-NPC1 (Abcam), anti-NPC2 (Abcam), anti-Lamp1 (BD biosciences), anti-Lamp2 (BD bioscience), anti-PIKfyve (Abnova), anti-Flag (Sigma), anti-HA (Invitrogen), and anti-Tubulin (Sigma), GAPDH (Abcam) or HSP90 (Palex) as loading controls in Western blot (WB) analysis. Anti-mouse IgG (GE Healthcare, Chicago, IL, USA) or anti-rabbit IgG (Bio-Rad) conjugated to horseradish peroxidase was used at a dilution of 1:5000 was used as secondary antibody. Finally, bands obtained after development with ECL reagent were detected on a Molecular Imager Chemidoc XRSplus imaging system. The bands were quantified by densitometry and the data normalized to control values using Image lab software (Bio-Rad).
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6

Immunoblotting and Immunofluorescence Antibodies

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Anti-p62/SQSTM1 (MBL, PM045), anti-β-actin (Sigma-Aldrich), anti-HA (Invitrogen), anti-ubiquitin (Santa Cruz Biotechnology, P4D1), anti-LC3B (Cell Signaling Technology, #2775), and anti-PrP (Santa Cruz Biotechnology, M20; SPI-Bio, SAF61 and SAF32; SIGNET, 3F4) antibodies were purchased from the indicated vendors. Horseradish peroxidase-conjugated anti-goat (Santa Cruz Biotechnology), anti-mouse and anti-rabbit IgG antibodies (GE Healthcare Life Sciences) were used for immunoblotting. Alexa Fluor® 488-conjugated anti–mouse IgG and Alexa Fluor® 594-conjugated anti–rabbit IgG antibodies (Invitrogen) were used for immunofluorescence analysis.
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7

In vivo CRISPR-Cas9 gene editing in mouse brain

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All the animal procedures were performed in accordance with University of Wisconsin guidelines. For in vivo injection, 1.5 μl of 1:2 AAV9 mixture of AAV9-APP-sgRNA:GFP (or AAV9-GFP) and AAV9-Cas9 was injected into the dentate gyrus (−2.0, ± 1.6, −1.9) of 8-week old male C57BL/6 mice (either sex)41 (link). Two-weeks after surgery, the mice were sacrificed by trans-cardiac perfusion of saline, followed by 4% PFA. The brains were dissected, post-fixed with 4% PFA overnight, immersed in 30% sucrose until saturation, and sectioned at 40 μm. Sections were immunostained with following antibodies: anti-HA (1:1000, 16B12), anti-GFP (1:1000, Invitrogen) and anti-APP (1:200, Y188). Images were acquired using Zeiss LSM800 confocal microscope. Average intensities of APP staining in cell bodies was quantified using Metamorph.
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8

Antibody List for Protein Analysis

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The following antibodies were purchased from Cell Signaling Technology: anti-IRS-1 (2382), anti-pAKT S473 (9271), anti-p85 (4292), anti-IGF-1Rβ (9750), anti-PDK1 (13037). Other antibodies were from the following commercial sources: anti-VAPB (Sigma-Aldrich, HPA013144), anti-NOGOA (Bio-Rad, AHP1799), anti-BAP31 (Santa Cruz Biotechnology, sc-48766), anti-PERK (abcam, ab229912), anti-pPERK (Affinity Biosciences, DF7576), anti-AKT (HUABIO, ET1609-47), anti-Actin (HUABIO, M1210-2), anti-Tubulin (HUABIO, M1305-2), anti-GFP (HUABIO, ET1607-31), anti-FLAG (YEASEN, 30503ES60), anti-HA (Invitrogen, PA1-985) and anti-mCherry (ABclonal, AE002).
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9

Antibody Localization in Toxoplasma

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The following primary antibodies were used in IFA or Western blot: anti-MIC2 [28 (link)], anti-GRA14 [33 (link)], anti-ROP7 (Monoclonal antibody [MAb] 1B10) [33 (link)], anti-SRS44, anti-IMC3 [34 (link)], mouse anti-ISP3 [10 (link)], anti-IMC1 mAb 45.15 [35 (link)], rat anti-RON11 [24 (link)], VVL-FITC (Vector laboratories), and biotinylated-VVL (Vector laboratories). Hemagglutinin (HA) epitope was detected with mAb HA.11 (Covance) and rabbit polyclonal anti-HA (Invitrogen). For localization of GRASP55, a fluorescent fusion was used as previously described [36 (link)].
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10

Immunoprecipitation of HA-tagged Proteins

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Sf9 cells were rinsed with ice-cold PBS and lysed with RIPA buffer (50 mM Tris, pH = 7.5, 1 mM EGTA, 1 mM EDTA, 1% Triton X-100, 150 mM NaCl, 2 mM DTT, 100 μM PMSF, 1 μg/ml Proteinase Inhibitors). The cell lysates were centrifuged at 20,817×g at 4°C for 10 min and the supernatants (WCL) were collected. The protein concentrations of the WCL were determined by Bradford assays and 1500 μg was mixed with 2 μg anti-Ha (Sigma) and Protein G Agarose (Millipore) and incubated at 4°C overnight according to the manufacturer’s protocol. The immunoprecipitated samples were centrifuged and washed three times and subjected to Western blot assays using anti-Ha (1:1000 dilution) and anti-EGFP (1:1000 dilution, Invitrogen).
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