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13 protocols using β3 tubulin

1

Protein Detection in Ischemic Brain

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To detect levels of proteins involved in inflammation and regeneration after brain ischemia, mice stroke affected lateral portions of the hemisphere were isolated and snap-frozen in liquid nitrogen and stored at −80 °C. Proteins were isolated by mechanical homogenisation in SDS-urea-β-mercaptoethanol solution containing proteinase inhibitor on ice. Electrophoresis and transfer on the PVDF-membrane was done using BioRad Mini-PROTEAN3 System (BioRad, Hercules, CA, USA).
Primary antibodies were β3-Tubulin (5568 S, Cell Signalling Technology, Beverly, MA, USA) as a loading control, DLG4 (PSD95) (3450, Cell Signalling Technology Beverly, MA, USA), GAP43 (AB5220, Merck, Kenilworth, NJ, USA), synaptophysin clone SY38 (MAB5258, Merck, Kenilworth, NJ, USA), and anti-cleaved CASP3 (Cell Signaling, Danvers, MA, USA). Secondary antibodies were goat anti-mouse, and goat anti-rabbit (32430 and A27011, Thermo Fisher Scientific, Waltham, MA, USA). The chemiluminiscent signal achieved by Western Lightning – EXL Enhanced Chemiluminiscence Substrate (Perkin Elmer, Waltham, MA, USA) was imaged by ChemiDoc MP System (BioRad, Hercules, CA, USA) and analysed using Image Lab Software (BioRad, Hercules, CA, USA).
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2

Immunofluorescence Analysis of hAFSCs

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For immunofluorescence analysis, hAFSCs from different fractions were processed, and confocal imaging was performed using a Nikon A1 confocal laser scanning microscope, as previously described [22 (link)].
Primary antibodies to detect Oct4, β3-Tubulin and SSEA4 (Cell Signaling, Danvers, MA, USA), Ki-67 (Santa Cruz Biotechnology, Santa Cruz, CA, USA), Runx2 (Abcam, Cambridge, UK), Osteocalcin and GFAP (Millipore, CA, USA), MAP2, nestin, CD29/Integrinβ1 and CD44/HCAM (Santa Cruz Biotechnology), CD271/NGFR (Sigma-Aldrich, St. Louis, MO, USA) were used following datasheet recommended dilutions. Alexa secondary antibodies (Thermo Fisher Scientific, Waltham, MA, USA) were used at 1:200 dilution.
The confocal serial sections were processed with ImageJ software to obtain three-dimensional projections. The image rendering was performed by Adobe Photoshop software.
The cell fluorescence signal was quantified using ImageJ and applying the following formula:
Corrected Total Cell Fluorescence (CTCF) = Integrated Density—(Area of selected cell X Mean fluorescence of background readings).
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3

Tracking Cell Migration in Wound Healing

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Wound tissues were sampled on days 3 and 17 after treatment, embedded in an optimal cutting temperature compound, frozen, and sliced into 10-µm-thick sections at − 22 °C. Sections were then treated with primary antibodies against rabbit anti-CD31 (Abcam) overnight at 4 °C, followed by a 50 min treatment with goat anti-rabbit IgG secondary antibody (Abcam) at 37 °C and 10 min treatment with 4′,6-diamidino-2-phenylindole (DAPI). The stained slides were observed under an Olympus VS200 fluorescence microscope (Japan). To visualize the migration of BMSCs and regenerated nerves in vivo, tissue sections on day 3 and 17 were stained with antibodies against CD90 (ProteinTech), nestin (ProteinTech), and β3-tubulin (Cell Signaling Technology). CD90, nestin, and β3-tubulin signals were visualized using FITC- and CY3-conjugated secondary antibodies (Thermo Pierce). Nuclei were stained with DAPI. Using a laser scanning confocal microscope (VS200, Olympus), images of the sections were obtained for three randomly selected areas for the quantification of fluorescence intensity. All images were post-processed and quantified using ImageJ software.
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4

Antibody and Plasmid Reagents for Neurological Research

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The following antibodies were purchased: CNTNAP2 (C-terminal, rabbit polyclonal, Millipore), CNTNAP2 (N-terminal, mouse monoclonal, Neuromab), actin (mouse monoclonal, Abcam), GFP (chicken polyclonal, Abcam), Flag (mouse monoclonal, Sigma-Aldrich), vGLUT1 (guinea pig polyclonal, Synaptic System Antibodies), PMCA2 (rabbit polyclonal, Thermo Fisher), β3-tubulin (rabbit monoclonal, Cell Signaling Technology), EEA1 (rabbit polyclonal, Cell Signaling Technology), PSD95 (rabbit monoclonal, Cell Signaling Technology), CaMKII, phospho Thr286 (rabbit polyclonal, Abcam), Neuroligin 1 (N-terminal, rabbit polyclonal, Alomone) and CNTN1 (N-terminal, goat polyclonal, Abcam). Plasmids used in this study were: pEGFP-N1 and DsRedExpress2 (Clontech); Flag-CNTNAP2 (generated by subcloning human CNTNAP2 cDNA from a plasmid kindly provided by Dr. Elior Peles, Weizmann Institute of Science, Israel) (Gao et al., 2018 (link)); PMCA2w/b, GCamP6s, CNTN4.2-Fc-His plasmids and AAV1.Syn.GCaMP6f.WPRE.SV40 (Addgene); shPMCA2 and scramble shRNA (VectorBuilder); and Fc-CNTNAP228–1261 (Rubio-Marrero et al., 2016 (link)). Lentiviral vectors for expression of shPMCA or scramble were packaged, and titered by the Northwestern GET iN Core.
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5

Immunofluorescence Analysis of Apoptosis and Cell Markers

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For immunofluorescence double staining, apoptosis was detected by the ApopTag Fluorescein In Situ Apoptosis Detection Kit (S7110; Chemicon International, Temecula, CA), as described previously15 (link). And then, sections were incubated overnight with cell surface glycoprotein F4/80 (Serotec, Oxford, UK) and a Texas red-labeled secondary antibody and counterstained with 4,6-diamidino-2-phenylindole (DAPI). We also performed immunofluorescence double staining for SOX10 (Abcam, Cambridge, UK), β3-tubulin (1:50; Cell Signaling Technology, Danvers, MA), and LC3 (1:200; Sigma-Aldrich, St. Louis, MO, USA). The fluorescent images were examined under a laser scanning confocal microscope system (Carl Zeiss LSM 700, Oberkochen, Germany).
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6

Antibodies and Assays for Cell Analysis

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Antibodies against JMJD2A, STMN1, β3-Tubulin, α-Tubulin and β-Tubulin were purchased from Cell Signaling Technology (Boston, USA). F-actin and PSA were purchased from Thermo Fisher (Shanghai, China), TUNEL Apoptosis Assay Kit from Beyotime (Shanghai, China), Phosphate-buffered saline (PBS) from Solarbio (Beijing, China), and Cell Counting Kit-8 from BBI Life Sciences (Shanghai, China).
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7

Aβ1-40 Regulation of Neuroinflammation

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The amyloid β protein fragment 1–40 (Aβ1−40), GW4869, PKH67, LPS and IFN-γ were purchased from Sigma (California, USA). Lipofectamine 2000 were purchased from Invitrogen (CA, USA). The antibodies GAPDH, YB-1, PTEN, NeuN and Iba1 were purchased from Abcam (Cambridge, MA), and the antibodies β3 tubulin, CD206, CD11b, Arg-1, iNOS were purchased from Cell Signaling Technology (Boston, Massachusetts). The ELISA kits were purchased from Blue gene (Shanghai, China). The YB-1 plasmids, miR-223 antagomir and miR-223 agomir were purchased from Genechem (Shanghai, China). The RiboCluster Profiler RIP-Assay Kit was purchased from MBL Medical & Biological Laboratories Co (LTD, Japan).
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8

Identifying Cell Types in Tissue Culture

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Cultured DRG neurons, Schwann cells, and fibroblasts were first fixed in 4% paraformaldehyde (Sigma-Aldrich) for 30 minutes. They were then incubated with bovine serum albumin (5%; from Invitrogen) for 1 hour at room temperature to block nonspecific binding. Then, the cells were incubated with antibodies to the fibroblast marker Thy-1 cell surface antigen (anti-CD90) (mouse, 1:1000, Abcam, Cambridge, MA, USA, Cat# ab225, RRID: AB_2203300), the Schwann cell marker S100 calcium-binding protein (Anti-S100) (rabbit, 1:1000, Sigma, Cat# SAB5500172) and the DRG neuron marker β3-tubulin (rabbit, 1:1000, Cell Signaling, Danvers, MA, USA, Cat# 5568S) at 4°C for 12–16 hours. Then, the cells were incubated with Alexa Fluor 594 goat anti-mouse IgG (1:400, Abcam, Cat# ab150116, RRID: AB_2650601) and goat anti-rabbit IgG H&L Alexa Fluor 488 (1:500, Abcam, Cat# ab150077, RRID: AB_2630356) secondary antibodies for 2 hours at room temperature. Nuclei were labeled with Hoechst 33342 (1:1000, Abcam, Cat# ab145597). The morphology of Schwann cells and fibroblasts was observed under a TCS SP2 confocal microscope and a Zeiss-ax10 fluorescence microscope (Carl Zeiss). Cell type and axon length statistics were confirmed using ImageJ 1.8.0 (National Institutes of Health, Bethesda, MD, USA; Schneider et al., 2012).
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9

Comprehensive Histological Analysis of Bone

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Following micro-CT test, the specimens were prepared (decalcified, dehydrated, paraffin-embedded, and sectioned). H&E and Masson's trichrome staining were performed. Immunohistochemical (IHC) staining was performed to detect CD206 (1:1000, Abcam), iNOS (1:1000, Abcam), CD31 (1:5000, Abcam), α-SMA (1:1000, Proteintech), TNF-α (1:100, Affinity), and IL-1β (1:200, Abcam). Tissue slices were captured using an Aperio AT2 scanning system (Leica, Germany). Immunofluorescence staining was performed using CGRP (1:100, Abcam), β3-Tubulin (1:200, Cell Signaling Technology), OCN (1:100, Santa Cruz Biotechnology) and collagen I (1:500, Thermo Fisher). Images were taken using CLSM. The quantitative analysis was performed using Image J software.
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10

Multimarker Immunofluorescence for Neural and Immune Cell Profiling

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For neuronal marker staining, sections were first repaired using ethylenediaminetetraacetic acid antigen retrieval solution (pH 9.0) for 5 min at 100°C and blocked with 3% BSA solution for 30 min. After rinsing, sections were probed overnight at 4°C with the following primary antibodies: β3-tubulin (1:200, Cell Signaling Technology) or Neurofilament-L (1:100, Cell Signaling Technology). Sections were then washed and incubated with Alexa Fluor 488 conjugated goat anti-rabbit or rabbit anti-mouse secondary antibodies (1:500, Invitrogen) for 1 h at 37°C, correspondingly.
To investigate the inflammatory response, immunofluorescence analysis of CD68 (1:1,000, Invitrogen) and CD206 (1:200, Proteintech) was performed similarly as earlier. Sections were then incubated with Alexa Fluor 647 conjugated goat anti-rabbit or Alexa Fluor 568 conjugated rabbit anti-mouse secondary antibodies (1:500, Invitrogen) for 1 h at 37°C, respectively.
To evaluate exosomes, CD63 primary antibody (1:200, Affinity) was selected and incubated with sections at 4°C overnight, then treated with Alexa Fluor 647 conjugated goat anti-rabbit secondary antibody.
Nuclei were counterstained with 4′,6-diamidino-2-phenylindole for 10 min. Sections were observed using a CLSM.
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