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6 protocols using β pix

1

Western Blot Analysis of Neuronal Proteins

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Equal amounts of samples measured with BCA assay (Thermo Scientific #23225), were loaded into Bolt 4–12% Bis-Tris gels (Life Technologies). Proteins were transferred to a PVDF membrane (Life Technologies) overnight, blocked with 5% milk (or 5% BSA for surface biotinylation), and incubated with primary antibodies against GABAAR β2/3 (Millipore #MAB341, 1:500), β-PIX (Millipore #07–1450-I, 1:1000), β-actin (Cell Signaling #4970, 1:1000), c-myc (Sigma-Aldrich #4439, 1:1000) and V5 (Cell Signaling #13202, 1:1000) either for 2 hour at room temperature or overnight at 4°C. For western blot experiments after Co-IP experiments that were done using primary neurons, secondary antibodies that were light chain specific were used to avoid imaging heavy chain of IgG (Jackson Immunoresearch Laboratories, #115–605-174; 1:800 and #211–602-171; 1:800). For western blot experiments after surface biotinylation, HRP-linked secondary antibody was used (Cell signaling, #7076, 1:2000). For the rest of the western blot experiments, Alexa Fluor-647 secondary IgG F(ab’)2 fragment antibodies (Cell Signaling, #4414 and #4410; 1:5000) were used. Secondary antibodies were incubated with membrane for 1 hour at room temperature. Blots were imaged using a Chemidoc MP imaging system (Bio Rad) and analyzed using the ImageJ 1.48 gel analyzer tool [53 (link)].
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2

Immunofluorescence and Western Blot Analysis of Cdc42, Rac1, and RhoA Signaling Pathways

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Primary antibodies were obtained targeting: Cdc42 (rabbit polyclonal, Cell Signaling), Rac1 (mouse monoclonal, Cytoskeleton), RhoA (mouse monoclonal, Santa Cruz), β-Pix (rabbit polyclonal, Millipore), Tuj1 (mouse monoclonal, Millipore), active Cdc42 (mouse monoclonal, New East Biosciences), Ret (pig anti-human, Abgent). The secondary antibodies used included: goat anti-mouse (Santa Cruz) and goat anti-rabbit (Santa Cruz). For western blots, cells were lysed with RIPA buffer (SantaCruz), boiled and separated by 3-8% Tris-Acetate SDS-PAGE.
For immunofluorescence microscopy, antibodies used included RET (rabbit monoclonal, Cell Signaling), p-Ret (phospho-Y1062, rabbit polyclonal, Abcam), β-Pix (SH3 domain, rabbit polyclonal, Millipore Sigma), and Cdc42 (rabbit polyclonal, Cell Signaling). Cells were fixed in 4% formaldehyde and permeabilized in 0.5% Triton X-100 (vol/vol), or fixed in 3.7% paraformaldehyde and blocked with 3% horse serum in 0.1% Triton in PBS for 60 minutes. The secondary antibody was Alexa Fluor 488 (goat anti-rabbit, Thermo Fisher Scientific). Slides were mounted with ProLong Diamond Antifade Mountant (Invitrogen, Thermo Fisher Scientific) and were scanned with a Flash Scanner (Perkin Elmer) and a Panoramic Viewer (3DHistech, Thermo Fisher Scientific) was used to capture images.
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3

Western Blot Analysis of Cell Signaling Proteins

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H9C2 cells and mouse hearts were stored at −80°C until use for western blotting.18 (link) Cells were lysed and then the extracts were cleared by centrifugation and stored at −80°C until use. The extracts were boiled in 2× Laemmli sample buffer. Samples were than subjected to SDS–polyacrylamide gel electrophoresis followed by western blot analysis using specific antibodies raised against Scrib (Santa Cruz), Vangl2 (Santa Cruz), Rac1 (Millipore), β-PIX (Millipore), Git1 (Novus Biologicals), or β-tubulin (Abcam). Horseradish peroxidase-conjugated secondary antibodies (Jackson ImmunoResearch Laboratories) were used for detection using the enhanced chemiluminescence method (GE Healthcare BioSciences). Quantification of protein levels was determined by densitometry using the ImageJ software. Band intensities were normalized to β-tubulin. The Kruskal–Wallis ANOVA test for non-parametric data was used for statistical analysis.
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4

Embryonic Heart Protein Interactions

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Embryonic hearts (E10.5) were homogenized in ice-cold NP-40 lysis buffer, and the lysates pre-cleared with protein G beads (Pierce, Thermo Scientific) and then incubated with the primary antibody [Scrib from Santa Cruz; Rac1 (Millipore); β-PIX (Millipore), β-catenin (BD Transduction Laboratories) at 4°C, overnight]. Lysates were incubated with protein G beads to precipitate complexes for 2 h at 4°C. The immunocomplexes were recovered by centrifugation, washed, precipitated, and denatured. Proteins were size separated by SDS–polyacrylamide gel electrophoresis and western blot analysis using antibodies as above.
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5

Immunohistochemistry of Cardiac Tissue

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Samples for immunohistochemistry were either fixed in PFA and paraffin-embedded or equilibrated through a sucrose series (to 15%) and subsequently mounted and frozen in OTC (Tissue-tek). In the latter case, air-dried sections were fixed with methanol or 4% PFA for immunostaining. Primary antibodies utilized were Scribble (Santa Cruz); Vangl2 (gift from Dr Charlotte Dean, London, UK), MF20 (DSHB), phospho-histone H3 (Millipore), cleaved caspase-3 (Cell Signalling), sarcomeric α actinin (Abcam), alpha-smooth muscle actin (α-SMA) (Sigma), cardiac troponin I (Hytest Ltd), Rac1 (Millipore), β-PIX (Millipore), β-catenin (BD Transduction Laboratories), N-cadherin (BD Transduction Laboratories), and connexin-43 (Chemicon). Alexa fluor 488 and 596-conjugated secondary antibodies (Invitrogen) were used to detect the primary antibody. Phalloidin (Sigma) was used to stain the actin cytoskeleton and wheat germ agglutinin (Alexa fluor 647; Invitrogen) was used to stain cell membranes. Cell nuclei were identified using DAPI. Immunofluorescence images were collected with using a Zeiss Axioimager Z1 fluorescence microscope equipped with Zeiss Apotome 2 (Zeiss, Germany). Acquired images were processed with the AxioVision Rel 4.9 software.
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6

Co-immunoprecipitation Protocol for HEK293T and Neurons

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For co-immunoprecipitation (co-IP) done with HEK293T cells, the cells were plated to reach 60–70% confluency for the day of transfection and after 24 hours of transfection, the cells were collected. For co-IP done with neurons, DIV8–9 cultures were used. For both cell lines and primary neurons, the samples were treated either with 50nM leptin or vehicle for indicated durations. The samples were lysed with cold TNE buffer (1% Nonidet P-40, 140 mM NaCl, 5 mM EDTA, and 50 mM Tris-HCl, pH 8.0) that was supplemented with cOmplete protease inhibitor cocktail and phosphatase inhibitor cocktail 2 and 3 (Sigma Aldrich) on ice for 20–30 min and the lysates were centrifuged for 10 min at 16,000g [32 (link)]. 10% of the lysate was separated as input and the rest of the lysate was incubated with c-myc (Sigma-Aldrich #4439, 1:100) and V5 (Cell Signaling #13202, 1:100) antibodies for HEK293T cells, and β-PIX (Millipore #07–1450-I, 1:100) antibody for neurons for 2 hours at 4°C, rotating. Then, they were incubated with Protein A/G magnetic beads for another 2 hours at 4°C, rotating. Supernatant was discarded and the beads were washed four times, each for 10 min, with TNE buffer. The samples were eluted with 50mM DTT (Fisher Scientific) and NuPage LDS Sample Buffer (Life Technologies), by heating at 75°C for 10 min and analyzed by western blotting.
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