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26 protocols using ab8049

1

Western Blot Analysis of Synaptic Proteins

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Five microgram of protein from either isolated synaptoneurosomes or crude homogenate was loaded onto NuPAGE 4–12% Bis‐Tris precast polyacrylamide 15 well gels (Invitrogen, Paisley, UK) along with molecular weight marker (Li‐Cor, Cambridge, UK). Proteins were electro‐transferred to nitrocellulose membrane (Bio‐Rad, Hemel Hempstead, UK). Membranes probed with the following primary antibodies: Aβ(82E1,IBL,1 : 100), Tau13 (MMS‐520R‐500, Covance, 1 : 2000), β‐actin (ab8226, Abcam, 1 : 2000), Synaptophysin (AB8049, Abcam, 1 : 10 000), α‐tubulin (ab4074, Abcam, 1 : 1000), GFAP (0334, DakoCytomation, 1 : 500), GAPDH (ab8245, Abcam, 1 : 2000). Proteins were visualized on an odyssey infrared system using the appropriate 680 and 800 IR dye secondary antibodies (1 : 50 000, LI‐COR Biosciences) and were analyzed using odyssey software (LI‐COR Biosciences).
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2

Neuromuscular Junction Morphology Analysis

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TA muscles were harvested and washed in ice-cold PBS, then fixed overnight in 4% paraformaldehyde at 4°C. The fixed muscle portions were separated into small bundles by gentle dissection using forceps and blocked overnight at 4°C in 5% goat serum, 5% BSA, and 2% Triton X-100 in PBS, then incubated with mouse anti-synaptophysin (1:25; ab8049, Abcam) and rabbit anti–neurofilament 200 (1:200; N4142, MilliporeSigma) overnight at 4°C to label presynaptic motor neuron terminals and axons, respectively. NMJ image stacks were obtained with a Leica SP8 confocal microscope with a 63× objective and analyzed using ImageJ (NIH). NMJ morphology was characterized for en face endplates using the following categories: (a) axon diameter, (b) number of nerve terminal branches, (c) number of nerve terminal branch points, (d) nerve terminal area, (e) percentage unoccupied AChR area, (f) synaptophysin compactness, and (g) end plate area. An average of 10 NMJs per animal were analyzed. All analyses were done by a single observer blinded to the identity of the sample. Full methodological details can be found in Supplemental Methods.
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3

Dual Immunolabeling of Rat Amygdala

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The control or NMD rats were deeply anesthetized with chloral hydrate and perfused transcardially with 0.9% isotonic saline followed by 4% paraformaldehyde (PFA) in saline. Then the brains were post fixed overnight in PFA. After that, the brains were transferred to a 20% sucrose solution followed by a 30% sucrose solution. For labeling, 12 μm sections of BLA were simultaneously incubated with synaptophysin (1:100, ab8049, Abcam) and TRPV1R (1:200, ACC-030, Alomone labs) antibodies for overnight at 4 °C and then incubated with secondary antibody with Alexa Fluor 488 and 594 for 2 hours at room temperature. Negative controls were performed without the primary antibody.
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4

Characterization of Hippocampal Proteins

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Hippocampal tissues and cultured neurons were lysed in buffer containing 25 mM HEPES at pH7.9, 150 mM NaCl, 1 mM PMSF, 20 mM NaF, 1 mM DTT, 0.1% NP40, and proteinase inhibitor cocktails (Roche). Protein concentrations were determined by Folin phenol method with bovine serum albumin as standard. Twenty micrograms of the protein was separated on 8–12% SDS-PAGE gels (Bio-Rad) and transferred to PVDF membranes (Millipore). The membranes were blocked in 5% BSA in TBS-T with 0.05% Tween-20 and incubated with primary antibodies at 4°C overnight. Dilutions of primary antibodies were 1:1000 for UTX (E409, Millipore), H3K27me3 (1:1,000, 07449, Millipore), PSD95 (ab2723, Abcam), Synapsin (ab8049, Abcam), and 1:10,000 for β-actin antibody (Sigma). As for the secondary antibodies, we used HRP-linked goat anti-mouse or HRP-Linked goat anti-rabbit at 1:500. Enhanced chemoluminescence (ECL, Pierce) was used for detection. Quantification of the blots was determined with Quantity One Ver.4.4.0 (BioRad, USA).
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5

Immunocytochemical Staining of Neuronal Markers

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ICC staining occurred as described previously13 (link). In brief, cells were first preblocked using DPBS containing 5% normal goat serum (Vector Laboratories) and 0.1% Triton X-100 for 30 minutes, followed by overnight incubation with primary antibodies: mouse microtubule-associated protein 2 (MAP2, 1:400; MAB3418; Millipore), mouse postsynaptic density protein 95 (PSD-95; 1:500; ab2723; Abcam), or mouse synaptophysin (1:300; ab8049; Abcam). After washing with DPBS, cells were incubated with secondary antibodies that included goat anti-mouse Alexa Fluor 568 (1:500; A11031; Invitrogen) or goat anti-mouse Alexa Fluor 488 (1:500; A11001; Invitrogen), followed by counterstaining with DAPI (D9542; Sigma-Aldrich). Coverslips were then mounted on slides with Mowiol mounting medium.
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6

Immunohistochemical Analysis of Tau and Gliosis

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The brain of each mouse was stored in 4% PFA overnight at 4°C and then incubated in a 30% sucrose solution for 24 h at 4°C. Samples were sectioned coronally at 40 μm using a freezing sliding microtome. Two to three sections (bregma -1.4 mm to -2.0 mm) from each mouse were used for free-floating p-tau staining. Brain sections were washed three times in 1X PBS followed by blocking with 5% donkey serum 1% BSA in 0.5% PBS-X (Triton X-100) for 1 h. The sections were incubated with the primary antibody AT8 (Thermo Scientific, MN1020, 1:1000) or anti-GFAP (Chemicon, MAB360, 1:1000) overnight at 4°C. The next day, the sections were washed three times in 1X PBS, and incubated with fluorescence-labeled secondary antibody Goat Anti-Mouse Alexa Fluor 488 (Abcam, ab150113, 1:1000) for 2 h at room temperature. The slices were then washed three times in 1X PBS and placed in mounting medium with DAPI and DABCO™ (EMS). For analysis of synapses, the brain sections were incubated with primary anti-Synaptophysin antibody (Abcam, ab8049, 1:50) for 48 h at 4°C and then incubated with secondary antibody (JIR, anti-mouse Cy™3, 1:500). Data analysis was performed with blinding to animal genotypes.
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7

Comprehensive Alzheimer's Disease Protein Analysis

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Sodium fluoride (Sigma-Aldrich, USA); mouse monoclonal anti-Aβ antibody (6E10, SIG-39340, BioLegend Inc., USA); rabbit polyclonal anti-C3 (complement component 3), rabbit polyclonal anti-Iba-1 (ionized calcium binding adaptor molecule 1), rabbit polyclonal anti-SNAP-25 (synaptosomal-associated protein 25) and mouse anti-BACE1 (β-site amyloid precursor protein cleavage enzyme 1) antibodies (GTX101316, GTX100042, GTX113839, and GTX78908, Gentex Inc., USA); mouse monoclonal anti-SYP (synaptophysin) and rabbit polyclonal anti-BACE2 antibodies (ab8049 and ab5670, Abcam Inc., USA); mouse monoclonal anti-ADAM10 (a disintegrin and metalloproteinase domain-containing protein 10) and mouse monoclonal anti-β-actin antibodies (sc-28358 and sc-376421, Santa Cruz Inc., USA); horseradish peroxidase-conjugated secondary antibody (7076s and 7074s, Cell signaling Inc., USA); kits for measuring malondialdehyde (MDA), superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) (A003-1, A001-1, and A005, Nanjing Jiancheng Bioengineering Institute, China); kits for measuring Aβ42 levels (KMB3441, Thermo Fisher Scientific, USA); and all other general chemicals (Sigma-Aldrich, USA) were purchased from the sources indicated.
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8

Molecular Markers for Alzheimer's Research

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We purchased the following materials from the sources indicated: PNU-282987 (Sigma-Aldrich, USA), anti-synaptosome-associated protein 25 (SNAP-25), anti-NRF2, and anti-HO-1 antibodies (GTX113839, GTX103322, GTX 101147, Gentex, Inc., USA), anti-synaptophysin (SYP), anti-β-site amyloid precursor protein-cleaving protein 1 (BACE1) anti-BACE 2 antibodies (ab8049, ab183612 and ab270458, Abcam, Inc., USA); anti-Aβ (6E10, SIG-39340, BioLegend, Inc., USA), and anti-β-actin, anti-α disintegrin, and metalloproteinase 10 (ADAM10) antibodies (sc-376421and sc-28358, Santa Cruz, Inc., USA).
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9

Comprehensive Brain Protein Extraction and Analysis

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Immediately after killing, mouse brains were dissected63 (link) in the specific brain regions olfactory bulb, hippocampus, striatum, cortex, midbrain, brain stem, cerebellum and the rest. Proteins of each region were extracted with RIPA buffer (10 mM Tris-Cl (pH 8.0), 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS and 140 mM NaCl) containing 1 × complete protease inhibitor cocktail (Roche, Indianapolis, IN). The protein concentrations in the supernatants were determined by the BCA method (Pierce Chemical Co., Rockford, IL) and equal amounts of protein lysates (∼20 μg per lane) resolved on 4–12% Bis-Tris SDS–PAGE gels with MES running buffer, then transferred to polyvinylidene difluoride (Invitrogen, Carlsbad, CA) membranes, and probed with following antibodies: anti-human tau polyclonal antiserum KJ9A (1:5,000; A0024, Dako Cooperation, Carpinteria, CA); Purified anti-Tau 316–355 monoclonal antibody 77G7 (1:1,000; BioLegend, San Diego, CA); rabbit anti-APP C-terminal (1:2,000; AB5352, Chemicon); monoclonal antibody against synaptophysin (1:1,000; AB8049, Abcam, Cambridge, MA); rabbit anti-GAPDH antiserum (1:5,000; G9545, Sigma); and monoclonal anti-β-tubulin III antiserum (1:10,000; T2200, Sigma). Immunoblots were developed using enhanced chemiluminescence method (Millipore Corp., MA).
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10

Quantification of Hippocampal Synaptic Proteins

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Hippocampal samples of six animals from each group were isolated and homogenized in a lysis buffer containing 50 mM Tris-HCl (pH 7.4),0.1% Triton X-100, 4 mM EGTA, 10 mM EDTA, and a tablet of protease and phosphatase inhibitors (Roche, Basel, Switzerland). A homogenized tissue was centrifuged at 12,000 rpm for 15 min at 4°C. Protein quantification was performed using the supernatant, following the method of Bradford (Bradford, 1976 (link)). Similar quantities of proteins from the homogenate were separated in a polyacrylamide gel (10% SDS-PAGE) and transferred to a nitrocellulose membrane. The unspecific binding was blocked with a 1% Tween-20 Tris buffer containing 2% bovine serum albumin for 1 h at room temperature. After that, the membrane was incubated with Ponceau S for 5 min for labeling of transferred proteins. The membranes were then washed and incubated overnight with primary antibodies for NMDA-2B (ab65783, Abcam, Cambridge, United Kingdom), Glu2/3/4 (2460S, Cell Signaling Technology, Danvers, MA, United States), CAMKIV (4032S, Cell Signaling Technology, Danvers, MA, United States), or synaptophysin (ab8049, Abcam, Cambridge, United Kingdom). On the following day, the membranes were incubated with a secondary antibody (Abcam, ab6721 Rb) for 2 h at room temperature, and protein density was quantified using the ImageJ software (Abramoff et al., 2004 ).
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