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110 protocols using psd95

1

Quantitative Synaptic Protein Analysis

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Whole cell lysates were obtained from the dissected hypothalami from WT controls and Fmr1 knockout mice. The same amount of protein from each sample, determined by Bradford assay, was resolved on SDS-PAGE, transferred on nitrocellulose membrane and probed for: GABAγ2 receptor subunit (1:1000, 14104-1-AP, Proteintech), NMDAR1 (1:1000, 32-0500 Invitrogen), NMDAR2B (1:1000, 07-632 EMD Millipore), postsynaptic density protein 95 (PSD-95; 1:1000, 3409, Cell Signaling), microtubule-associated protein 2 (MAP2; 1:5000, ab5392, Abcam) or β-tubulin (1:1000, sc-9104, Santa Cruz Biotechnology). Bands were quantified using ChemiDoc imaging system (Bio-Rad, Hercules, CA).
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2

Western Blot Analysis of Synaptic Proteins

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Tissue samples were homogenized in 1% SDS processing buffer and protein was quantified using the Bio-Rad protein DC assay (Bio-Rad Laboratories, Berkeley, CA, USA). Forty μg of total protein was loaded onto a 12–15% polyacylamide gradient gel (Mini-PROTEAN TGX Precast Mini Gel, Bio-Rad Laboratories) and transferred to a nitrocellulose membrane. Membranes were blocked in 5% non-fat dried milk or BSA (phospho-FMRP) in TBS, incubated overnight in primary antibodies against PSD-95 (1:1,000; Cell Signaling, Beverly, MA, USA), SAPAP-3 (1:500, ProteinTech, Chicago, IL, USA), FMRP (1:500, Millipore, Billerica, MA, USA), phospho-FMRP (1:1,000; Abcam, Cambridge, MA, USA), and GAPDH (1:30,000; Millipore) diluted in TBS + 0.1% Tween 20 (Sigma-Aldrich, St. Louis, MO, USA). The following day, membranes were incubated for 1 hr in the appropriate secondary antibodies (1:20,000; Li-Cor Biosciences, Lincoln, NE, USA) and then imaged using the Odyssey imaging system (LiCor Biosciences).
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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

Protein Quantification and Western Blot Analysis

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Total protein in Tris-buffered saline (TBS) and neutralized formic acid (FA) extracts was quantified using the Ready to Use Bradford Reagent (Bio-Rad) and for TBS-Triton X100 (TBSX) extracts the BCA Protein Assay Kit (Pierce).
For western blot analysis of TBS-X fractions protein (20 μg) was separated on 4–12 % Bis-Tris gels (Invitrogen) and transferred onto low-fluorescence PVDF membranes. Membranes were blocked (1 hr. room temperature) with 5 % non-fat milk in TBS containing 0.1 % Tween 20 (TBST), then incubated (4 °C, overnight) with primary antibodies against post synaptic density protein (PSD-95, 1:1000, Cell Signaling), synaptophysin (1:1000, Cell Signaling), the EGF receptor (1:100, Santa Cruz Biotechnology) or actin (1 hr. room temperature, 1: 20,000, Cell Signaling) in TBST with 5 % bovine serum albumin (BSA). Membranes were incubated in secondary antibodies (Jackson Immunoresearch) with TBST wash (3X5min) in between steps and imaged using an Odyssey ® Fc Imaging System. Image J was utilized to quantify actin normalized proteins.
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5

Hippocampal Protein Expression Analysis

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Protein was extracted from mice's hippocampal tissue. Protein lysates were separated by 12% SDS-PAGE electrophoresis and transferred onto polyvinylidene difluoride (PVDF) membranes. After blocking with 3% BSA for 1 h, the membranes were incubated with primary antibodies. CAMKII (Cell Signaling Technology, 7546, 1 : 500), P-CaMK-II (Cell Signaling Technology, 9546, 1 : 500), P-CREB (Cell Signaling Technology, 9198 s, 1 : 500), CREB (Cell Signaling Technology, 9197, 1 : 500), PKA (Proteintech, 55388-1-AP, 1 : 1000), NMDAR1 (Cell Signaling Technology, 5104 s, 1 : 1000), BDNF (Cell Signaling Technology, 47808, 1 : 1000), PSD95 (Cell Signaling Technology, #2507, 1 : 1000), GAPDH (Proteintech, 6004-1-lg, 1 : 2000) and Tubulin (Proteintech, 10094-1-AP, 1 : 2000) were used at 4°C overnight. The next day, blots were washed 4 times in TBST, followed by incubation with secondary antibodies for 1 h. After washing for 3 times, the blots were visualized using the Super Signal West Pico Chemiluminescent Substrate (Thermo Fisher Scientific Inc.). BDNF and pro-BDNF were normalized to Tubulin bands, and P-CERB and total CREB bands were taken as a ratio of Tubulin bands. All experiments were performed 3 times.
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6

Dendritic Complexity Analysis of Hippocampal Neurons

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Hippocampal neuronal cells were rinsed with phosphate buffered saline (PBS), fixed in 4% paraformaldehyde for 8 min and permeabilized with 0.1% Triton X-100 in PBS for 30 min. After being blocked with 5% milk for 30 min, the cells were incubated with primary antibodies conjugated to Alexa Fluor®488 or 594 against microtubule-associated protein-2 (MAP2, Abcam, 1:250) and PSD-95 (Cell Signaling, 1:250) at 4 °C overnight. The secondary antibody was then incubated at room temperature for 1 h and rinsed in PBS three times. The nuclei were stained with DAPI (Sigma) for 5 min. Fluorescence images were obtained using a BX53 Olympus fluorescence microscope at 20 × magnification and captured using Olympus CellSens Standard software. Sholl analysis was applied to measure dendritic complexity. The length of dendritic arborization was analyzed and measured using a semi-automatized protocol via Imaris software (Bitplane, Inc.).
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7

Hippocampal Membrane Protein Analysis

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The two hippocampi were pooled from each freshly dissected mouse and the membrane fraction was isolated using the Mem Per Plus kit (Thermo Fisher Scientific, Waltham, MA). Protein concentration was determined using the BCA protein assay (Thermo Fisher Scientific, Waltham, MA). 20 μg protein was loaded on 4–12% Bis-TRIS gels and were transferred to a PVDF membrane. Proteins were detected using antibodies for 5-HT5A (LifeSpan Biosciences, Seattle, WA), β-Actin and PSD-95 (both from Cell Signaling).
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8

Proteomic Analysis of Cerebral Cortex

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Whole-cell protein extracts were obtained from the ipsilateral cerebral cortices (+1 to −4 mm from bregma). Brain tissues were homogenized in cold RIPA buffer (50 mM Tris-HCI with pH 8.0, 150 mM NaCI, 0.5% sodium deoxycholate, 0.1% SDS, 1 mM EDTA, 1% NP-40) containing protease inhibitor (Pierce tablet; Thermo Fisher Scientific, A32965) and phosphatase inhibitor (Sigma, P0044). The homogenates were centrifuged at 13,000 rpm for 20 min at 4°C, and the supernatants were used for analysis. Protein content was measured using Bradford dye reagent (Bio-Rad, Hercules, CA). Protein samples (30 μg protein per sample) were separated by 4-20% gradient SDS-PAGE (Invitrogen) and transferred to PVDF membranes. The following primary antibodies were used: rabbit anti-LC3B (1:2000; Novus Biological, NB100-2220), rabbit anti-p62 (1:1000), mouse anti-CTSD (1:100),mouse anti-GAPDH (1:10000; Sigma, G8795), rabbit anti-postsynaptic density 95 (PSD-95; 1:1000; Cell Signaling, 3409), and mouse anti-β-actin (1:800; Sigma, A2066). Immunopositive bands of horseradish peroxidase-conjugated secondary antibodies were detected with an ECL system (GE Healthcare) and exposure to ECL Hyperfilm.
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9

Oxidative Stress and Neuroprotection Assay

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tBHP, D-gal, AlCl3, and glutamate were purchased from Sigma-Aldrich (St. Louis, MO). Kits used for MDA, SOD, glutathione (GSH), the bicinchoninic acid (BCA) protein assay, the ROS assay, and mitochondrial membrane potential detection were purchased from Beyotime (Shanghai, China). Antibodies against Nrf2, HO-1, SOD2, NQO-1, and Lamin B1 were obtained from Abcam (Cambridge, MA). Antibodies against β-actin, phospho-p38, p38, phospho-ERK, ERK, phospho-JNK, GAPDH, SYN, PSD95, Bcl-2, and Bax were purchased from Cell Signaling Technology (Beverly, MA). All secondary antibodies (horseradish peroxidase-conjugated anti-rabbit IgG and anti-mouse IgG) were purchased from Cell Signaling Technology (Beverly, MA). All reagents used were of the highest grade available commercially.
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10

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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