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19 protocols using 5 bromo 4 chloro 3 indolyl phosphate

1

Detecting IgE-reactive Pollen Proteins

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Pollen extracts (20 μL each) were separated on 15%, for ragweed, mugwort, and sawtooth oak, and 18%, for Japanese hop, sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions. After the separation of proteins, gels were stained with Coomassie blue or transferred onto polyvinylidene difluoride membranes (GE Waters & Process Technologies, Trevose, PA, USA). IgE reactive components were detected with pooled patients’ sera (1:4, n = 10) and alkaline phosphate conjugated goat anti-human IgE (1:1,000) (ε-chain specific, Sigma-Aldrich). The color was developed with nitroblue tetrazolium and 3-bromo-4-chloro-5-indolyl-phosphate (Promega, Madison, WI, USA).
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2

SDS-PAGE and Western Blot Analysis

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Recombinant protein or buckwheat extract was run on a 15% acrylamide gel containing SDS under reducing or non-reducing conditions. The gel was stained with Coomassie blue or transferred to a polyvinylidine difluoride membrane (0.45 µm; Millipore, Bedford, MA, USA). The membrane was blocked overnight with 3% skim milk in Tris-buffered saline containing 0.05% Tween 20. Subsequently, membranes were reacted with hybridoma culture supernatant and then incubated with 1:1,000-diluted goat anti-mouse IgE conjugated with alkaline phosphatase (Sigma-Aldrich). Color was developed with 3-bromo-4-chloro-5-indolyl-phosphate, and nitro blue tetrazolium as a substrate (Promega, Madison, WI, USA).
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3

Western Blot Analysis of XPress-YcgZ

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After separation on a 16% acrylamide gel, the proteins were electro-transferred to a nitrocellulose membrane (Millipore, Billerica, MA, United States). The membrane was incubated overnight at 4°C in Tris-borate-saline (TBS) buffer supplemented with 3% milk powder. The membrane was then incubated for 2 h at room temperature with monoclonal anti-XPress antibodies (Thermo Fisher Scientific) diluted in TBS (1/6,000). After three 15 min washes with TTBS (TBS supplemented with 0.05% Tween 20), the membrane was incubated for 2 h with alkaline phosphatase-coupled anti-mouse IgG antibodies (Promega) diluted 1/10,000 in TBS followed by three 15 min washes with TTBS and two 5 min washes with TBS. XPress-YcgZ was visualized by adding 5-bromo-4-chloro-3-indolyl phosphate and nitroblue tetrazolium following the manufacturer’s instructions (Promega).
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4

SDS-PAGE Analysis of Allergen Extracts

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Allergen extracts (20 μg) were run on 18% SDS-PAGE gel under reducing conditions and stained with Coomassie brilliant blue or transferred to a polyvinylidene difluoride membrane (Micro Separation Inc., Westborough, MA, USA). After blocking with 3% skim milk, the membrane was incubated with 1:4 diluted sera. Subsequently, it was incubated with 1:1,000 diluted alkaline phosphatase-conjugated goat anti-human IgE (Sigma-Aldrich, St. Louis, MO, USA). Nitro blue tetrazolium and 5-bromo-4-chloro-3-indolyl-phosphate (Promega, Madison, WI, USA) was used for color development. For inhibition analysis, 10 μg/mL of recombinant Bet v 1a (Indoor Biotechnologies Inc., Charlottesville, VA, USA) was pre-incubated with pooled sera (1:4 diluted) overnight. IgE reactive components were detected as described above.
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5

Identifying Heat-Stable Proteins

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To analyze heat-stable proteins, the protein extract was placed in boiling water for 5 min. Denatured or aggregated fraction after heat treatment was regarded as the heat-labile fraction, while the supernatant was considered to contain heat-stable proteins. Aggregated proteins were resuspended in PBS and separated on 10% or 12% SDS-polyacrylamide gels under reducing conditions along with the supernatant. IgE reactive components were probed with pooled serum samples (1:4 diluted). IgE antibodies were detected with alkaline phosphatase-conjugated goat anti-human IgE (1:1,000) (Sigma-Aldrich) for 1 hr. Color development was initiated by adding nitro blue tetrazolium and 5-bromo-4-chloro-3-indolyl-phosphate (Promega, Madison, WI, USA).
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6

Protein Extraction and Quantification

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Total protein was prepared from leaves and roots of plants grown for 2 weeks on GM agar medium (Valvekens et al., 1988 (link)). Tissues were ground under liquid nitrogen and homogenized in the extraction buffer [50 mM Tris-MES (pH 7.5), 300 mM sucrose, 150 mM NaCl, 10 mM CH3COOK, 5 mM EDTA, 20 μM leupeptine, 100 μM 4-(2-aminoethyl)benzenesulfonyl fluoride, 1 mM phenylmethylsulfonyl fluoride]. The lysate was centrifuged at 10,000 g for 15 min, and the supernatant was collected. Protein concentrations were determined using a Bio-Rad protein assaying kit (Bio-Rad) based on the Bradford method (Bradford, 1976 (link)), using bovine serum albumin as a standard. Proteins were separated in 10% (w/v) polyacrylamide gel, and transferred to Immobilon-P membrane (Millipore) by electroblotting. Ten micrograms of crude proteins were loaded to each lane of the gels. The blot was incubated with anti-GFP mouse monoclonal antibody (Nacalai Tesque, Japan), followed by incubation with goat anti-mouse IgG conjugated to alkaline phosphatase (Promega). The presence of immuno-reactive protein was detected through the use of 5-bromo-4-chloro-3-indolyl-phosphate and nitro blue tetrazolium (Promega).
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7

Immunoblotting Analysis of Bacterial Chemotaxis Proteins

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Cells were pelleted by centrifugation (6000 x g) and resuspended at an OD600 of 2 in 10 mM potassium phosphate (pH 7.0) and 0.1 mM EDTA. Cells from 0.5 ml of the suspension were pelleted and lysed by boiling in 50 μl of sample buffer (Laemmli, 1970 (link)). Proteins released from the lysed cells were analysed by electrophoresis in sodium dodecyl sulphate-containing polyacrylamide gels (SDS-PAGE) and visualized by immunoblotting with an antiserum directed against the highly conserved portion of the Tsr signalling domain (Ames and Parkinson, 1994 (link)) in 10% acrylamide, 0.05% bisacrylamide gels (Studdert and Parkinson, 2004 (link)), or an antiserum against CheW in 17.5% acrylamide, 0.47% bisacrylamide gels (Cardozo et al., 2010 (link)). Either Cy5-labeled (Amersham) or alkaline phosphatase-conjugated (Sigma) goat anti-rabbit immunoglobulin were used as secondary antibodies. Cy5-labeled antibodies were detected with a Storm 840 fluorimager (Amersham); alkaline phosphatase-conjugated antibodies were developed with nitro blue tetrazolium and 5-bromo-4-chloro-3-indolyl phosphate (both from Promega) and converted to grey scale images with a digital scanner. All gel images were analysed with ImageQuant (Amersham).
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8

Protein Expression Analysis in C. glutamicum

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C. glutamicum strains W, GAD, and GADΔpknG were cultured in test tubes at 30°C for 24 hours in 5 mL BHI medium containing 25 μg mL−1 kanamycin. Each culture (0.2 mL) was transferred to 20 mL BHI medium containing 25 μg mL−1 kanamycin in a 200 mL shaker flask. After fermentation for 24 hours, the cells from a 1 mL culture were centrifuged at 8,000 × g for 5 min, washed once in 50 mM Tris–HCl (pH 6.8) buffer, suspended in 1 mL of this buffer, and then 0.7 g of 0.1-mm diameter glass beads YGB01 (Yasui Kikai, Japan) was added to the tube. The cells were disrupted using a Shake Master Neo (Bio Medical Science) by shaking the tube three times at 1,500 rpm for 1 min at 1-min intervals. After centrifugation at 9,000 × g for 5 min, the supernatants were subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis. The separated proteins were electroblotted onto a polyvinylidene fluoride membrane (Millipore, Boston, MA, USA) and then reacted sequentially with a mouse anti-FLAG M2 monoclonal antibody (Sigma, St. Louis, MO, USA) and a goat anti-mouse IgG alkaline phosphate conjugate (Promega) secondary antibody. The membrane was stained with 4-nitro-blue tetrazolium chloride (Promega) and 5-bromo-4-chloro-3-indolyl phosphate (Promega) according to the manufacturer’s instructions.
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9

Beetle Tissue Protein Analysis

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Total proteins from different tissues of male and female beetles, including antennae, head (without antennae), thorax, abdomen, leg, and wing tissues, were extracted and standardized to 7.5 μg per sample. After electrophoretic separation, protein bands were trans-ferred from a 15% SDS-PAGE to a nitrocellulose membrane (0.2 μm, Millipore, United States), as described by Kyhse-Andersen (1984) (link). After treatment with 0.2% non-fat dry milk and 0.05% Tween-20 in PBS overnight, the nitrocellulose membrane was then incubated with the primary antiserum obtained previously at a dilution of 1:5000 based on the ELASA result in Supplementary Figure S1. Goat anti-rabbit IgG- horseradish peroxi-dase conjugate (diluted by 1:1000; Fermentas, MD, United States) was used as the secondary antibody. Immunoreactions were visualized by adding 5-bromo-4-chloro-3- indolyl-phosphate and 4-chloro-1-naphthol (Promega, WI, United States).
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10

Immunoblot Analysis of D. farinae Allergens

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D. farinae protein extract was separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) using a 15% gel. Standardized D. farinae protein extract was kindly provided by the Yonsei Allergy Institute.13 (link) Separated proteins were transferred to polyvinylidene difluoride membranes (0.45 µm, GE Water & Process Technologies, Trevose, PA, USA) to react with three groups of patient sera (five randomly chosen patients from each group). For inhibition of non-specific binding, the membranes were incubated in 3% skim milk overnight before overnight sera incubation at 37℃. As a secondary antibody, 1:1000 diluted mouse anti-human IgE and IgG4 (Southern Biotech, Birmingham, AL, USA) were incubated for 1 hour. Nitro blue tetrazolium and 5-bromo-4-chloro-3-indolyl-phosphate (Promega, Madison, WI, USA) were used for color development.
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