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65 protocols using westernbright quantum

1

Monitoring Wzc-Wzb Dephosphorylation by Western Blot

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The dephosphorylation reaction was monitored by Western immunoblot analysis. For that, 1 µg of both His6‐Wzc and His6‐Wzb was incubated in 20 µl of reaction buffer (100 mM sodium citrate, pH 6.5, and 1 mM EDTA) at 30°C for 0, 1, 2, 4, 6, 12, or 24 hr. Reactions were terminated by adding SDS‐PAGE sample buffer. Samples were heated at 95°C for 5 min, separated on 4%–15% SDS‐PAGE gels (Bio‐Rad), and transferred onto nitrocellulose membranes as previously described (Leitao, Oxelfelt, Oliveira, Moradas‐Ferreira, & Tamagnini, 2005). Membranes were probed with either monoclonal anti‐phosphotyrosine antibody (PT‐66; Sigma) diluted 1:2,000, or 6x‐His Epitope Tag Antibody (Thermo Scientific) diluted 1:1,000. Membranes were then incubated with goat anti‐mouse IgG‐HRP (Santa Cruz Biotechnology) at a dilution of 1:5,000. Immunodetection was performed using the ECLTM Western blotting detection reagents (GE healthcare) or the WesternBrightTM Quantum (Advansta) and a Chemi DocTM XRS+Imager (Bio‐Rad). The relative signal intensity of the bands obtained by immunodetection was quantified using the Image Lab software (Bio‐Rad). Data were statistically analyzed as described below.
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2

Antibody Detection of Iripin-8 in Tick Saliva

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Serum with antibodies against Iripin-8 was produced by immunization of a rabbit with pure recombinant protein as described previously [84 (link)]. Tick saliva was collected from ticks fed for 6 days on guinea pigs by pilocarpine induction as described previously [85 (link)]. Tick saliva was separated by reducing electrophoresis using NuPAGE™ 4–12% Bis-Tris gels. Proteins were either visualized using Coomassie staining or transferred onto PVDF membranes (Thermo Fisher Scientific). Subsequently, membranes were blocked in 5% skimmed milk in Tris-buffered saline (TBS) with 0.1% Tween 20 (TBS T) for 1 h at laboratory temperature. Membranes were then incubated with rabbit anti-Iripin-8 serum diluted in 5% skimmed milk in TBS-T (1:100) overnight at 4 °C. After washing in TBS-T, the membranes were incubated with secondary antibody (goat anti-rabbit) conjugated with horseradish peroxidase (Cell Signaling Technology; Danvers, MA, USA; 1:2000). Proteins were visualized using the enhanced chemiluminescent substrate WesternBrightTM Quantum (Advansta, San Jose, CA, USA) and detected using a CCD imaging system (Uvitec, Cambridge, UK).
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3

Quantitative Western Blot Analysis

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Western blots of whole cell lysates were performed in Lämmli buffer at 25 mA, using TRIS–glycine buffer for transfer 3 h at 100 mA at 4 °C. The membranes were stained with Ponceau S for quality control and marker labeling, blocked in 5% milk powder in PBS-Tween and after primary (O/N at 4 °C) and secondary antibody (1 h) incubation and three times washing in between. The blots were developed using the ECL substrate Western Bright Quantum (Advansta) on an ImageQuant LAS-4000 system (Fuji). The analysis was done in Open FiJi with the gel analysis tool. Shortly, the signal was measured as the area under the profile of intensity of each band over the surrounding background. Then, the signal ratio of each band with respect to its corresponding loading control (Actin or GADPH) was calculated. Calculations, plotting, and statistical analysis were done in Excel and GraphPad Prism software 9.0.
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4

Western Blot Analysis of Nuclear Proteins

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Western blot assays of resolved nuclear protein extracts were done with the antibodies listed in Text S1. Blots were visualized with WesternBright Quantum (Advansta) and quantitated with a G:BOX Chemi XT4 (Syngene; GeneTools 4.03.02.0v software).
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5

Quantitative Protein Analysis in mSKPs

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The mSKPs receiving various treatments were centrifuged and collected. Collected mSKPs were lysed by Passive lysis buffer (Promega, Madison, WI, USA). Protein was quantified using the Pierce BCA protein assay kit (Thermo Fisher Scientific). Equal amounts of protein (30‐50 μg) from each treated group were analysed on a 12% sodium dodecyl sulphate polyacrylamide gel. After transfer to a nitrocellulose membrane, the membrane was incubated with primary and secondary antibodies on a shaker. Detection was performed using WesternBright™ Quantum (Advansta, Menlo Park, CA, USA), according to the manufacturer's recommended protocol. Western blot data were analysed using the GeneGnome XRQ System (Syngene, Cambridge, UK).
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6

Sciatic Nerve Western Blot Analysis

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Western blots were performed as previously described (Sasaki et al., 2018 (link)). Sciatic nerves were quickly dissected and then placed in chilled PBS as the epineurium was removed. The nerves were then flash frozen and stored at −80°C. Sciatic nerves from postnatal day 7 mice were sonicated in ice-cold lysis buffer (50 mm Tris-HCl, pH 7.5, 150 mm NaCl, 10 mm EDTA, 10 mm NaF, 0.1% SDS, 1% Triton X-100, 1% deoxycholate, 1% NP-40, and 100 mm PMSF with protease inhibitors, Roche Diagnostics; and phosphatase inhibitors, Sigma-Aldrich). Lysates were centrifuged at 12,000 × g for 20 min at 4°C, supernatant was collected, and 10–20 μg of protein was boiled for 5 min in sample buffer with β-mercaptoethanol, loaded onto 10% SDS-PAGE gels, and then transferred onto nitrocellulose or PVDF membranes. Membranes were blocked in blocking solution (Super Block T20, Thermo Fisher Scientific) and then incubated with antibodies (Table 2) diluted in blocking solution. Membranes were washed, incubated in species-appropriate secondary antibodies (Cell Signaling Technology), and then developed using Western Bright Quantum (Advansta). Band intensity was measured using ImageJ (National Institutes of Health), normalized to α-tubulin or β-actin, and then displayed as fold change relative to the average of the WT samples.
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7

Quantification of Urinary Mucosa Proteome

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Urinary mucosa, defined as urothelium and lamina propria, was surgically separated from the smooth muscle, homogenized using Lysing Matrix D in a FastPrep 24 instrument (MP Biomedicals, Solon, OH) following previously established protocols.14 (link) Equal amounts of proteins were separated on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gels and transferred to polyvinylidene fluoride membranes, which were then incubated overnight at 4°C with primary antibodies (Table 1) followed by secondary antibodies (donkey anti-rabbit horseradish peroxidase [1:5000] or sheep anti-mouse horseradish peroxidase [1:5000]; GE Amersham, Pittsburgh, PA) for 1 hour in 5% (w/v) milk TBS-T, incubated in WesternBright Quantum (Advansta, Menlo Park, CA) and then imaged on a ChemiDoc MP (Bio-Rad). As a loading control, total protein per sample was determined using Bio-Rad Stain Free SDS-PAGE gel technology (Bio-Rad). UV-activated protein fluorescence was imaged on a ChemiDoc MP (Bio-Rad). Assessment of protein carbonylation (as a marker for oxidative damage) was performed with an antibody that detects dinitrophenylhydrazine (DNPH)-derivatized carbonyl groups (OxyBlot Protein Oxidation Detection Kit, S7150; Millipore, Burlington, MA).
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8

Fibroblast Protein Extraction and Western Blot Analysis

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Fibroblast cultures derived from HCF-1cKO or control C57BL/6 mice were mock infected or infected with Ad-Cre or Ad-FLPe. At 3.5 days postinfection, cells were lysed, and protein extracts were prepared using radioimmunoprecipitation assay (RIPA) buffer (50 mM Tris-HCl [pH 7.5], 250 mM NaCl, 1 mM EDTA, 1% NP40, 1% sodium deoxycholate (DOC), 0.1% SDS, cOmplete protease inhibitors, 2 mM NaV04, 1 mM NaF, 10 mM B-glycerophosphate). Western blots were done using antibodies to HCF-1 and control actin (Table S1), visualized with WesternBright Quantum (Advansta; catalog number K-12042-D20), and bands were quantitated using Syngene G:Box Chemi XT4 (Syngene; GeneTools 4.03.02.0v software).
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9

Western Blot Analysis of FXIII-A Variants

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To check the expression of FXIII-A variants, cells were lysed directly in SDS-Laemmli buffer (SDS-LB) (200 lL per 10 6 cells). Proteins were separated by electrophoresis on 7.5% polyacrylamide gel (all reagents from Sigma-Aldrich), and blotted onto polyvinylidene difluoride membranes (Carl Roth, Karlsruhe, Germany) in Tris-glycine buffer with 20% methanol. A primary monoclonal anti-FXIII-A antibody (ab1834; Abcam, Cambridge, UK), a secondary horseradish peroxidase-conjugated anti-mouse antibody (Pierce) and a chemiluminescence substrate (Western Bright Quantum; Advansta, Menlo Park, CA, USA) were used for detection.
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10

Western Blot Analysis of RECQ5 and GEN1

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Cells were lysed in Laemmli buffer [10% sodium dodecyl sulfate (SDS), 300 mM Tris-HCl, 10 mM β-mercaptoethanol, 50% glycine, 0.02% bromophenol blue]. Protein extracts were loaded in equal amounts for SDS-polyacrylamide gel electrophoresis and the separated proteins were transferred to a nitrocellulose membrane, blocked for 1 h at RT in Rotiblock (Roth) and incubated with primary antibodies overnight at 4 °C (anti-RECQ5, Abcam, ab91422 and ab224135 and anti-GEN1, Abgent, AP9493a and the antibodies described above). Membranes were then washed with 0.1% tween-tris-buffered saline and incubated with horseradish peroxidase-conjugated secondary antibodies for 1 h at RT. Immunoblots were developed using WesternBright Quantum or Sirius Kits (Advansta) and signal detection was performed with Fusion FX system (VilberLourmat).
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