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74 protocols using synaptophysin

1

Synaptic protein analysis in brain tissue

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Brain tissue was rapidly dissected out from hippocampus and temporal cortex and flash frozen in liquid nitrogen. Tissue samples were homogenized in RIPA buffer with protease and phosphatase inhibitors (Roche). Samples were centrifuged, and protein was collected from supernatant. Primary antibodies were PSD-95 (ThermoFisher, MA1-045) at 1:1000, synaptophysin (Abcam, ab32127) at 1:1000, beta-actin (mAbcam 8226) at 1:5000. Secondary antibodies were HRP-tagged anti-mouse and anti-rabbit (Santa Cruz) 1:5000. Group size was 3.
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2

Hippocampal Protein Expression Analysis

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Four mice per group were anesthetized with intraperitoneal injections of zoletil (90 mg/kg) and xylazine (10 mg/kg), and their hippocampi were collected. The extracted proteins were quantified by the BCA Protein Assay System (Pierce, USA). The proteins were subjected to SDS-PAGE, followed by electro-transfer to PVDF membranes (Millipore, USA). After blocking with 5% skim milk in 0.1% Tris-buffered saline (TBS)/Tween-20, the blots were probed with primary antibodies against GluA1 (1:1000, Abcam), GluN1 (1:1000, Sigma-Aldrich), GluN2A (1:2000, Millipore), NR2B (1:500, BD Transduction Laboratories), and synaptophysin (1:4000, Abcam) overnight at 4 °C. After incubation, the membranes were subsequently incubated for 2 h at room temperature with the appropriate secondary antibodies conjugated with horseradish peroxidase (Vector, USA). The proteins were visualized with an enhanced chemiluminescence kit (Pierce, USA) and band intensities were quantified using the Kodak Gel Logic 2200 imaging system with Molecular Image analysis software (Kodak, USA). β-Actin was used as a loading control (1:10000, Sigma-Aldrich). Data are presented as an average of at least three experiments and analyzed for statistical significance by using Mann-Whitney tests (Prism; Graph Pad, USA).
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3

Array Tomography for Synaptic Quantification

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The tissue was processed for array tomography as described in Micheva and Smith (20 (link)). Visual cortex was dissected from perfused animals and embedded in LR white resin using a bench top protocol. Ribbons with between 70–100 serial 70 nm ultrathin sections were prepared from P30 Mecp2-KO, WT and Mecp2-KO/NR2A-Het mice using an ultramicrotome (UC7, Leica Microsystems) and mounted side by side on subbed glass coverslips. Coverslips were immunostained using synapsin I (mouse, SYSY), synaptophysin (mouse, Abcam), PSD-95 (rabbit, Cell Signaling Technology), GluR1 (rabbit, Millipore), GluR2/3 (rabbit, Abcam), GluN2A or GluN2B (rabbit, Frontier Science Co., Ltd) and parvalbumin (guinea pig, Frontier Science Co., Ltd) antibodies. For secondary antibodies, Alexa 488, Alexa 594 and Alexa 647 (Invitrogen) were used from the appropriate species. For some ribbons, applied antibodies were eluted and the sections were restrained with different antibodies. The identification and quantification of GluN2A- and 2B-positive synapses is described in Figure 2 (A–D) and in further detail in the Supplemental Methods.
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4

Western Blot Analysis of Neuronal Proteins

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Cell and brain samples were lysed using a sonicator (Qsonica), and were subjected to Sodium dodecyl sulfate polyacrylamide gel electrophoresis (Bio-Rad). Separated proteins were transferred onto PVDF membranes (Bio-Rad) for Western blotting, and then hybridized with the primary antibodies, including P-ERK (Cell Signaling; 1:1,000 dilution), T-ERK (Cell Signaling; 1:2,000 dilution), P-GAP43 (Abcam; 1:1,000 dilution), T-GAP43 (Genetex; 1:5,000 dilution), PSD95 (Abcam; 1:5,000 dilution), Synaptophysin (Abcam; 1:5,000 dilution), VAMP1 (Abcam; 1:5,000 dilution), RANBP10 (Proteintech; 1:2,000), Flag M5 (Sigma; 1:2,000 dilution), mEM48 (a gift from Dr. Xiao-Jiang Li, Emory University, USA; 1:50 dilution), MAB2166 (Millipore; 1:2,000 dilution) and γ-tubulin (Sigma; 1:10,000 dilution) antibodies. Protein expression levels were determined by an Amersham ECL kit (PerkinElmer) through an imaging system (ChampGel), and expression profiling was quantitated by an ImageJ system (NIH).
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5

Synaptic Marker Co-localization Analysis

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Synaptic marker co-localization analysis was performed with the Imaris software (Oxford Instruments) as described previously42 (link),44 . Briefly, synaptophysin (Abcam) and PSD95 (Millipore), respective markers for pre- and post-synaptic terminals, were stained in mouse brain sections as described above. Sections were imaged with a 63X oil objective with a 4.0 digital zoom on a Leica confocal microscope. 5 μm thick Z stacks with 0.2 um step size were obtained. Using the Imaris’ ‘Spots’ feature, puncta from each channel were analyzed by generation of spot representation (automatic generation with consistent manual adjustment for all images for accuracy). Total number of spots for each channel were recorded. Spots were then analyzed using the ‘Co-localize Spots’ MATLAB plugin, defining co-localization if the center of the pre- and post-synaptic puncta were within 200 nm.
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6

Streptozotocin-Induced Diabetes Model

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Streptozotocin (STZ, 98% purity) was obtained from Sigma-Aldrich Chemical Company (St. Louis, MO, USA), as were total cholesterol (TC) and triglyceride (TG). Insulin was obtained from Linco Research, USA. Nitric oxide (NO) was obtained from Bio Systems S.A. Glucose, thiobarbituric acid reactive substances (TBARS), reduced glutathione (GSH), superoxide dismutase (SOD), and glutathione peroxidase (GPx) were obtained from Biodiagnostic Co. (Cairo, Egypt). Synaptophysin and Ki67 antibodies were obtained from Abcam Co. (Cambridge, UK). Other reagents were purchased from MyBioSource Co. (San Diego, USA). Daiwa Pharmaceutical Co. Ltd. (Tokyo, Japan) kindly provided Biobran (99% purity).
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7

Molecular Profiling of Neuronal Regeneration

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The distal end of the nerve, muscles, dorsal root ganglion cells, and brain (hippocampus/cortex) were harvested 4 weeks after the various treatment and proteins were extracted. The cell lysate of dorsal root ganglion cells after electrical stimulation were collected to determine the expression of synaptophysin, TNF-α, and NGF. Proteins (50 μg) were resolved by SDS–polyacrylamide gel electrophoresis and were transferred onto a blotting membrane [20 (link)]. After blocking with non-fat milk, the membranes were incubated with antibodies against S-100 (Neomarkers, 1:500 dilution), NF (Cellsignal, 1:1000 dilution), synaptophysin (Abcam, 1:500 dilution), TNF-α (Abcam, 1:1000 dilution), and NGF-R (1:1000, Abbiotec) overnight at 4 °C. The intensity of the protein bands was determined by a computer image analysis system (IS1000, Alpha Innotech Corporation, CA, USA).
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8

Antibody Panel for Neurodegenerative Markers

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The following antibodies were purchased from Abcam: BHMT (#ab96415), CD68 (#ab955), Rbm25 (#ab72237), Synaptophysin (#ab32127). Cell signaling: β-actin (#4967), Pin1 (#3722), PSD95 (#3409). Millipore: anti-Aβ42 (#5078P), 6E10 (#MAB1560), APP C-terminal (#171610). Santa Cruz Biotechnology: H2-Ab1 (#sc-71201). Wako: Iba1 (NCNP24).
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9

Immunofluorescence Analysis of Postnatal Mouse Brain

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Eight weeks old animals were transcardially perfused with 4% PFA/0.1 M PBS followed by 2 h post fixation with 4% PFA/0.1 M PBS. Postnatal day 7 (P7) brains were fixed for 6 h in 4% PFA/0.1 M PBS. Free-floating 30 μm sagittal brain sections were permeabilized and blocked for 1 h in PBS/0.5% Triton X-100/5% normal goat serum (NGS). Next, samples were incubated O/N at 4 °C with primary antibody solution in blocking buffer. After washing 3 times with PBS/0.2% Triton X-100, corresponding goat secondary antibodies (Alexa Fluor, Invitrogen) were diluted 1:500 in PBS/0.2% Triton X-100/2% NGS and incubated for 1 h at RT. Nuclear staining (Hoechst 33342 1:2000, Invitrogen) or myelin dye (Fluoromyelin red 1:300, Invitrogen) were incubated together with secondary antibodies. Sections were washed twice with PBS/0.2% Triton X-100 and once with PBS before being mounted using Fluoromount (Sigma Aldrich). Imaging was performed on 3 mice per genotype and time point using a Leica SP5 confocal microscope. Primary antibodies and dilutions were as follows: Calbindin (1:500, Swant); CD68 (1:500, AbD Serotec); Iba1 (1:300, Wako); NeuN (1:500, Millipore); CNPase (1:300, Abcam) and Synaptophysin (1:500, Abcam).
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10

Comprehensive Antibody and Reagent Protocol

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The following antibodies were purchased from the indicated vendors: E2F1 KH20 (sc-56662); E2F1 KH95 (sc-251); GAPDH (sc-32233) [Santa Cruz], Doublecortin (AB2253); vGluT1 (AB5905); Tyrosine hydroxylase (AB152); PSD-95 (MAB1596) [Millipore], OMP (#544-10001) [Wako]. NMDAR1 (#5704); NMDAR2A (#4205); NMDAR2B (#4212); Synapsin (#5297); GluR2 (#2460); ERK1/2 (#4695); E2F1 (#3742); Lamin A/C (#2032); α-tubulin (#2125) [Cell Signaling], Synaptophysin (ab8049); MAP2 (ab5392) [Abcam], actin (A2066) [Sigma]; SV2 [DSHB]. The following chemical reagents were used from the indicated vendors: DAPI [Molecular Probes]; Coomassie (161-0786); Protein assay dye (500-0005), PVDF membrane [BioRad], Fast Green FCF; protease inhibitor cocktail [Sigma], Pageruler plus protein ladder [Thermos], Luminata Forte Western HRP substrate [Millipore]. All HRP conjugated secondary antibodies were obtained from Pierce and all dye conjugated secondary antibodies were obtained from Jackson Immuno-Research.
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