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29 protocols using ab32136

1

Immunofluorescence and TUNEL Staining of Coronal Brain Slices

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Coronal brain slices prepared as described above were blocked and incubated with an anti-Iba1 (1:500; Abcam, ab178846) or anti-β-amyloid (Aβ) (1:500; Abcam, ab32136) antibody overnight at 4 °C and then with Alexa Fluor 488-conjugated goat anti-rabbit IgG (1:1000, Life Technologies) for 1 h at room temperature and counterstained with 4ʹ,6-diamidino-2-phenylindole (DAPI). Fluorescence signals were visualized with a laser scanning confocal microscope (Zeiss, Oberkochen, Germany). To measure hippocampal apoptosis, brain sections were subjected to TUNEL staining (Thermo Fisher) and counterstained with DAPI following the manufacturer’s instructions.
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2

Antibody Optimization for Western Blot and PLA

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Primary antibodies for PLA and western blotting are described in Table 1. Secondary antibodies (horseradish peroxidase (HRP)-Goat anti-mouse and HRP-Goat anti-rabbit) were purchased from Bio-Rad and GE Healthcare. Secondary antibodies conjugated to PLA probes were purchased from Sigma-Aldrich (Merck).

List of antibodies used for western blotting (WB) and proximity ligation assay (PLA)

Antibody nameCompanyDilution (WB)Dilution (PLA)
Anti-ADAM10Abcam (ab39153)1:40001:4000
Anti-Amyloid beta precursor protein C-terminus [Y188]Abcam (ab32136)1:50001:5000
Anti-APP C-terminus [C1/6.1]BioLegend (802801)1:1000
Anti-BACE1Cell Signaling Technology (D10E5)1:10001:200
Anti-PSD-95Abcam (ab2723)1:20 000
Anti-PSD-95Neuromab, k28/43 (75-028)1:1000
Anti-SynaptophysinEnzo (VAM-SV011F)1:10 0001:3000
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3

Alzheimer's Protein Biomarkers Quantification

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Mice were euthanized and brains perfused and removed as above, after which they were either lysed using 1 ml of protein lysis buffer (50 mM NaCl, 20 mM HEPES, 1 mM EDTA, 2% Triton-X 100, 10% glycerol, with proteinase and phosphatase inhibitor) to extract total protein or 1 ml of TRIZol solution to extract RNA. NF-κB, Ikb-α, APP, beta secretase 1 (BACE-1), and presenilin 1 (PS1) levels were detected using western blot (4–12% Nupage Bis-Tris gel, Thermo Fisher Scientific) using standard technique (antibody: #8242S, #9242S, 1:1000, Cell signaling, Danvers, MA; ab 32136, 1:5000, Abcam; ab 2077, 1:1000, Abcam; MAB 5232, 1:1000, Millipore Sigma, Burlington, MA). Uncropped western blots in main figures are shown in Supplementary Figure 7. Relative expression of mRNA for APP was detected by two-step, real-time quantitative reverse transcription-PCR (RT-PCR) with the ABI Perkin Elmer Prism 5700 Sequence Detection System (Applied Biosystems, Foster City, CA) using Taqman probe (Mm00476361, Mm01344172, Invitrogen, Carlsbad, CA).
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4

Multimodal Immunofluorescence Imaging of PTEN and APP in Brain Tissue

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The rats were deeply anesthetized and perfused with 0.9% saline and 4% paraformaldehyde. The isolated brain was fixed in 4% paraformaldehyde for 24 h and dehydrated using sucrose (20%, 30%) for 24 h. Then, it was embedded in an OCT compound for cryosection and cut into 10 μm thick coronal sections. Next, fluorescent immunolabeling was performed according to the standard indirect technique as described previously. Primary antibodies used included PTEN (ab79156, 1:100, Abcam, Cambridge, MA, USA), β-APP (ab32136, 1:100, Abcam, Cambridge, MA, USA) and β III Tubulin (sc-51670, 1:200, Santa Cruz, Dallas, TX, USA). After washing three times in PBS, Dylight 488 conjugated Goat Anti-Rabbit IgG (A23220, 1:100, Abbkine, CA, USA) and Dylight 594 conjugated Goat Anti-Rat IgG (A23440, 1:100, Abbkine, CA, USA) were added to PBS containing 1% BSA for 1 h. In the final wash, 6-diamidino-2-phenylindole (DAPI) (28718-90-3, 1:100, Abbkine, CA, USA) was added and used as a counterstain for the nucleus. A ZEISS confocal laser scanning microscope was used to obtain fluorescence images (ZEISS LSM700, GER). PTEN+/β-APP+, in which positive cells were counted in 5 randomly selected regions (100×) of each slice using ImageJ software. Immunofluorescence staining was performed for five brains.
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5

Quantifying Spinal Cord Protein Expression

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A spinal cord segment, 0.5 cm in length, from where the injured site was centered
was used for protein quantification using western blotting. Proteins of the
nucleus and cytosol were extracted using the NE-PER Nuclear and Cytoplasmic
Extractions Kit (Thermo Fisher Scientific, Waltham, MA, USA), following the
manufacturer’s instructions. The protein mixture extracted from each segment was
separated via electrophoresis and transferred to the polyvinylidene difluoride
membrane (Bio-Rad Laboratories, Hercules, CA, USA). The membranes were first
incubated with PFKFB3 (1:5,000, ab181861, Abcam, Cambridge, UK), Bax (1:1,000,
ab32503, Abcam), Bcl-2 (1:500, ab59348, Abcam), cleaved caspase-3 (CC-3, 1:500,
ab13847, Abcam), p-CDK1 (1:1,000, ab201008, Abcam), p27 (1:5,000, ab32034,
Abcam), H3 (1:5,000, ab1791, Abcam), myelin basic protein (MBP) (1:1,000,
ab209328, Abcam), APP (1:1,000, ab32136, Abcam), β-actin (1:5,000, ab8226,
Abcam), and p-p27 (1:1,000, ab75908, Abcam) antibodies at 4°C overnight,
respectively, and incubated with the secondary antibodies (1:10,000, ZB-2301 or
ZB-2305, Zhongshan Gold Bridge, Beijing, China) at 25°C for 1 h. The proteins
were detected using an ECL kit (Immobilon, Millipore, Billerica, MA, USA). The
gray values of each band were calibrated according to the internal reference and
compared to those of the sham group to acquire a relative value.
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6

Western Blot Analysis of Lipid Metabolism

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Cells grown to near confluence on 6 cm-dishes were lysed, separated by SDS gel electrophoresis and blotted onto polyvinylidene difluoride membranes. Antibodies directed against Abca1 (ab18180), LDL receptor (ab30532), HMG-CoA reductase (ab174830), SREBP-2 active fragment (ab30682), NPC1 (ab134113), and APP (ab32136) were obtained from Abcam (Cambridge, UK). Antibodies to AMPKα (#2603 S) and phospho-Thr172-AMPKα (#2535 S) were from Cell Signaling Technology (Danvers, MA, USA), while anti-β-actin (A5441) was from Sigma-Aldrich Chemie GmbH (Taufkirchen, Germany). HRP-conjugated secondary antibodies were from GE Healthcare (Freiburg, Germany). The enhanced chemiluminescence system was from Millipore Corporation (Billerica, MA, USA).
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7

Alzheimer's Disease Pathology Analysis

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Thioflavin-S was obtained from Sigma-Aldrich (T1892). The inhibitor of ubiquitin proteasome system, MG-132 (S, R, S), the inhibitor of Transforming growth factor β (TGF-β) signaling pathway, SB431542 and the inhibitor of mammalian target of rapamycin (mTOR) signaling pathway, rapamycin (Sirolimus) were all purchased from Selleck (Houston, TX, USA). MG-132, SB431542 and rapamycin were all dissolved in Dimethyl sulfoxide (DMSO) and added to the medium 1 h before the treatment of brain extracts. Corresponding with the DMSO content of each treatment, DMSO at a final concentration of 0.5% was added in the control groups. The primary antibodies were: mouse anti-Aβ1–16 (6E10; SIG-39320, Covance, Princeton, NJ, USA), rabbit anti-APP (Ab32136, Abcam, UK), rabbit anti-APP C-terminal fragments (CTF; A8717, Sigma-Aldrich, St. Louis, MO, USA), rabbit anti-β secretase (anti-BACE1; 5606S, Cell Signal, Danvers, MA, USA), mouse anti-β-actin (C4, Santa Cruz, Dallas, TX, USA), rabbit anti-glial fibrillary acidic protein (anti-GFAP; AB5804, Millipore, USA), mouse anti-GFAP (3670S, Cell Signal, Danvers, MA, USA), rabbit anti-ionized calcium binding adapter molecule 1 (anti-Iba1; 019-19741, Wako, Japan), mouse anti-t-Tau (Tau-5, Millipore, USA) and rabbit anti-p-Tau (pSer202, Life-Span BioSciences, San Jose, CA, USA).
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8

Clathrin and AP2 Immunoprecipitation Assay

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For the Clathrin and AP2 immunoprecipitation (IP) assays, protein samples were added to Dynabeads-Protein G (30 μg/100 μL) according to the manufacturer protocol (Invitrogen, DK).
The following were used for both WB and IP analysis: rabbit monoclonal (Y188) antibody to APP (ab32136, Abcam, UK), mouse anti-alpha adaptin antibody (AP6) specific against AP2 (MA1-064, Thermo Fisher, DK), mouse anti-Clathrin heavy chain antibody (clone X22) (MA1-065, Thermo Fisher, DK). Rabbit, anti-AP1+2 antibody (ab21981) were provided by Abcam.
APP pTyr residues were immunoprecipitated using anti-pTyr antibody clone 4G10® agarose conjugate (clone 16-10, Millipore) and analyzed with rabbit anti-APP (clone Y188) following the same procedures previously reported (Matrone et al., 2011 (link)). Rabbit anti-pan Fyn (#4023) and anti-Src pTyr416 (#2101) and anti-Src pTyr527 (#2105) were provided by Cell Signaling Technology (BioNordika, DK).
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9

Antibody Resources for Neurodegenerative Research

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Antibodies against full length APP (ab32136), BACE2 (ab8025), glucagon (ab10988), IDE (ab32216) and the insulin receptor (ab69508) were purchased from Abcam (Cambridge, UK). Antibodies against insulin (L6B10), p-GSK3β (D3A4), GSK3β (D5C5Z), p-AKT (193H12) and AKT (C67E7) were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA). The monoclonal 4G8 antibody targeting the Aβ peptide used in these studies was purchased from Covance (Princeton, NJ, USA) and is now available from Biolegend (San Diego, CA, USA). Antibodies against the N-terminus of APP (MAB348), GLUT2 (07-1402), and GLUT4 (07-1404) were purchased from Millipore (Darmstadt, Germany). Antibodies against GLUT1 (sc-7903), GLUT3 (sc-7682), and ZNT8 (sc-98243) were purchased from Santa Cruz Biotechnology, Inc. (Dallas, TX, USA).The antibody for amylin (250470) was purchased from Abbiotec (San Diego, CA, USA). The antibody against human APP (803001) was purchased from Biolegend (San Diego, CA, USA). The antibody against Aβ oligomers (11610) was purchased from Cayman Chemical (Ann Arbor, MI, USA). The antibody against neprilysin (MAB1126) was purchased from R&D Systems (Minneapolis, MN, USA).
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10

Alzheimer's Disease Protein Detection Protocol

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Maintain diet and 2% of HMD were obtained from Synergetic Pharmaceutical Bioengineedring Co., Lt. (China). HMD was prepared by adding 2% Met to the Maintain diet. Amyloid precursor protein (APP, ab32136), beta-secretase 1 (BACE1, ab108394), insulin-degrading enzyme (IDE, ab109538), amyloid-β 1-42 (Aβ1-42, ab201061), DNA methyltransferase1 (DNMT1, ab188453), and DNA methyltransferase 3a (DNMT3a, ab188470) antibodies were purchased from Abcam (UK). Amyloid-β 1-40 (Aβ1-40, D8Q7I) and 5-mC (D3S2Z) antibodies were obtained from Cell Signaling Technology (USA). Neprilysin (NEP, D161012) antibody was obtained from Sangong Biotech (China). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, 10494-1-AP) and β-actin (66009-1-Ig) antibodies were obtained from Proteintech (China). HRP-conjugated affinipure goat anti-rabbit IgG (SA00001-2), HRP-conjugated affinipure goat anti-mouse IgG (SA00001-1), and CoraLite488- conjugated affinipure goat anti-rabbit IgG (SA00013-2) were obtained from Proteintech (China).
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