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58 protocols using mms 101p

1

Gq-DREADD Expression in Perirhinal Cortex

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Under the same plane of anesthesia the Gq-DREADD (AAV2-hSyn-HA-hM3D(Gq)-IRES mCitrine, Bryan Roth, University of North Carolina, Chapel Hill, NC) was microinjected into the perirhinal cortex (coordinates measured from bregma at the skull surface, angled 10° laterally, as follows: anterior–posterior (AP) −4.8 mm, medial-lateral (ML) −5 mm, DV −7.5mm). Gq-DREADDs were allowed 3 wk to reach maximal expression levels before CNO testing began. AAV was microinjected in a volume of 0.75 µL/side (1012 IU/mL) at a rate of 0.1 µL/min, allowing 10 min for diffusion.
Following the last test session, rats were transcardially perfused with 10% buffered formalin, and brains were removed for immunohistochemistry on free-floating (40 µm) sections. Tissue was treated with peroxidase, then blocked with 2% normal donkey serum in PBS. Sections were incubated overnight at 4°C in primary antibody: mouse anti-hemagglutinin (HA) (1:1000; Covance #MMS101-P, RRID: AB_2314672). The secondary antibody was biotin-SP conjugated donkey anti-mouse IgG (1:500; Jackson ImmunoResearch Laboratories). The signal was amplified with an avidin-biotin complex (1:500), then reacted with diaminobenzidine (in 5% nickel). Tissue was mounted onto slides, dehydrated, cover-slipped, and examined under a microscope to visualize the Gq-DREADD.
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2

Antibody Dilution Protocol for Western Blotting

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All antibodies were used at a 1:1000 dilution in TBST (tris-buffered saline–Tween 20) buffer with 5% nonfat milk for Western blotting. Anti–phospho-Ser473-Akt antibody (4060), anti-Akt1 antibody (2938), anti–total Akt antibody (4691), anti–phospho-S6 antibody (4858), anti-S6 antibody (2217), anti–phospho-eIF4B (Ser406) antibody (8151), anti-eIF4B antibody (3592), anti–His-tag antibody (12698), anti–phospho-S6K1 (Thr389) antibody (9205), and anti-S6K1 antibody (2708) were obtained from Cell Signaling Technology. Polyclonal anti-HA antibody (sc-805) was obtained from Santa Cruz Biotechnology. Anti-tubulin antibody (T-5168), anti-HA agarose beads (A-2095), peroxidase-conjugated anti-mouse secondary antibody (A-4416), and peroxidase-conjugated anti-rabbit secondary antibody (A-4914) were obtained from Sigma. Monoclonal anti-HA antibody (MMS-101P) was obtained from Covance.
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3

Seliciclib, a CDK2 Inhibitor, in Lung Cancer

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Seliciclib (CYC202, R-roscovitine) was provided by Cyclacel, Ltd (10mM stock solution in dimethyl sulfoxide, DMSO). The seliciclib dosage used (10μM) is clinically achievable (34 (link)) and biological effects of seliciclib at 10μM were due to CDK2 inhibition rather than CDK7/9 blockade in lung cancer cells (19 (link)). Antibodies used were: α-tubulin (T6199, Sigma Aldrich, (1:1000 immunofluorescence and 1:10000 immunoblot), α-tubulin (YL1/2) (NB600-506, Novus Biologicals, 1:1500), γ-tubulin (T5326, Sigma Aldrich, 1:1000), CP110 (12780-1-AP, Proteintech, 1:750), HA.11 clone 16B12 monoclonal antibody (MMS-101P, Covance, 1:3000), cyclin F (C-20) (SC-952, Santa Cruz Biotechnology, 1:500), CEP76 (A302-326A, Bethyl Laboratories, 1:1000), USP33 (A300-925A, Bethyl Laboratories, 1:1000 in 5%BSA) and KRAS (ab55391, Abcam, 1:1000). Secondary antibodies used were: Texas red anti-mouse IgG (H+L) (TI-2000, Vector Laboratories.), Fluorescein anti-mouse IgG (H+L) (FI-2000, Vector Laboratories.), Alexa fluor 594 donkey anti-rat IgG (H+L) (A21209, Invitrogen), ECL anti-rabbit lgG (NA934V, GE Healthcare), ECL anti-mouse lgG (NA931V, GE Healthcare) and horseradish peroxidaseconjugated donkey anti-goat IgG (sc-2020, Santa Cruz Biotechnology.). Hoechst 33342 (62249, Thermo Scientific, 1:25000) stained DNA. Pro-Long Gold anti-fade reagent (P36934, Invitrogen) preserved immunofluorescence.
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4

Antibody Validation for Protein Studies

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These antibodies were purchased: sheep polyclonal anti-PCDH15 (Cat.# AF6279; R&D Systems); mouse monoclonal anti-HA (MMS-101p; Covance) and anti-FLAG (clone M2; Sigma-Aldrich); Alexa Fluor 488-conjugated (Cat.# ab181448; Abcam) and Alexa Fluor 647-conjugated (Cat.# ab150115; Abcam) goat anti-mouse IgG; biotinylated (Cat.# 65-6140; Thermo Fisher) and Alexa Fluor 647-conjugated (Cat.# ab150079; Abcam) goat anti-rabbit IgG; Alexa Fluor 488-conjugated donkey anti-sheep IgG (Cat.#ab150177); and biotinylated donkey anti-rabbit IgG (Cat.# A16027; Thermo Fisher).
The following homemade antibodies were used in this study: rabbit anti-TMC1 serum (against N-terminal 39 aa residues of human TMC1) (Li et al., 2019) (link), anti-GFP serum (against purified GFP), and anti-LHFPL5 serum (against C-terminal 20 aa residues of human LHFPL5; Yu et al., Under Revision). The antibodies were generated by immunizing rabbits housed in the animal care facility at the Hong Kong University of Science and Technology.
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5

Immunofluorescence Imaging of SLC1A2/A3 Cells

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SLC1A2/A3-expressing HEK293 Flip-In cells were plated on poly-L-lysine hydrobromide (Sigma-Aldrich)–coated glass coverslips and induced with doxycycline (1 μg/ml) where indicated. After 24 h, cells were washed with PBS, fixed (PBS, 2% formaldehyde), and permeabilized (PBS, 0.3% saposin, 10% FBS). Slides were incubated with anti-HA (MMS-101P; Covance) and anti-AIF (5318; Cell Signaling) antibodies (1 h, RT, PBS, 0.3% saposin, 10% FBS). After three washes, slides were incubated with Alexa-Fluor-488–coupled anti-mouse (A11001; Life Technologies) and Alexa-Fluor-594–coupled anti-rabbit (A11012; Life Technologies) (1 h, RT, PBS, 0.3% saposin, 10% FBS). After DAPI staining, slides were washed three times and mounted on coverslips with ProLong Gold (Invitrogen). Images were taken with a Zeiss Laser Scanning Microscope (LSM) 700.
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6

Sorafenib and Rapamycin Anticancer Protocol

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Sorafenib was purchased from LC labs, Rapamycin was purchased from MedChemExpress. Antibodies against HA (MMS101P, Covance), FLAG (F1804, Sigma), GST (IT003 M, M&C Gene Technology), His (66005-1-Ig, Proteintech), TGN46 (13573-1-AP Proteintech), AFP (4550-1-AP, Proteintech), GP73(sc-365817, Santa Cruz), E-cadherin (sc-8426, Santa Cruz), N-cadherin (22018-1-AP, Proteintech), MMP9 (10375-2-AP, Proteintech), PTEN (9188, CST), p-AKT (4060, CST), AKT (9272, CST), β-actin (AC026, ABclonal).
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7

Immunofluorescence Imaging of Transgenic mES Cells

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mES cells were transduced with Gm6871-HA, ZFP809-HA, or LacZ-HA and cultured with 5 μg/mL doxycycline. Cells were fixed in methanol for 10 min and labeled with anti-HA antibody (MMS-101P, Covance) followed by Alexa488-conjugated anti-mouse antibody. Nuclei were stained with DAPI. Images were acquired using a 63× lens on a Zeiss Axiovert 200M microscope.
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8

Detailed Antibody and Reagent Usage

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The following antibodies were used as follows: monoclonal SEZ6 (Pigoni et al, 2016), polyclonal SEZ6 (Gunnersen et al, 2007), pAb SEZ6L2 (R&D Systems, AF4916), pAb SEZ6L (R&D Systems, AF4804), GluR6/7 (04‐921, Millipore, GluK2 and GluK3 antibodies commercially available are not able to discriminate between these two subunits due to their high homology), NMDAR2b (D15B3, Cell Signaling), anti‐GluR2 (MAB397, Millipore), 3D5 (kindly provided by Robert Vassar), calnexin (Enzo, Stressgen, Farmingdale, NY, USA, ADI‐SPA‐860), β‐tubulin (T8578, Sigma), β‐actin (Sigma, A5316), PSD 95 (2507, Cell Signaling), LDLR (R&D Systems, AF2255), NCAM‐1 (R&D Systems, AF6070), rat mAb Flag M2 (F1804, Sigma), 5F8 anti‐Red (Chromotek), anti‐HA.11 (MMS‐101P, Covance), HRP‐coupled anti‐mouse and anti‐rabbit secondary (DAKO), and HRP‐coupled anti‐goat, anti‐rat, and anti‐sheep (Santa Cruz).
The following reagents and media were used as follows: neurobasal medium, HBSS and B27 (Invitrogen), C3 (β‐secretase inhibitor IV; Calbiochem, 565788, final concentration 2 μM), DMEM (Gibco), and FBS (Thermo Fisher Scientific).
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9

Western Blotting of Whole-Head Lysates

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We prepared whole-head lysates from 30 male heads per 100 μl radioimmunoprecipitation assay (RIPA) buffer (150 mM NaCl, 1.0% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 50 mM Tris–HCl, pH 8.0), including 1 mM dithiothreitol (DTT), 1 mM phenylmethanesulfonylfluoride (PMSF) and protease inhibitor mixed tablet (Roche). We mixed approximately 25 μg protein per sample with 6 X sample buffer containing SDS and β-mercaptoethanol and loaded samples on 12.5% SDS-PAGE gels, which we then transferred to a 0.2 μm pore size polyvinylidene difluoride membrane (Bio-Rad). Primary antibodies included anti-actin (Millipore; MAB1501; 1:40,000), and anti-HA (Covance; MMS-101P; 1:750). The secondary antibody used was horseradish peroxidase (HRP)-conjugated goat anti-mouse (Abcam; ab5930; 1:6,000). Both technical replicates and biological replicates were performed for each analysis and are presented as supplemental figures. We performed densitometry using ImageJ analysis software (US National Institutes of Health, Bethesda, MD, USA).
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10

Whole Cell Lysate Preparation and Immunoblotting

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Whole cell lysates were harvested by using EBC buffer (50 mM Tris pH8.0, 120 mM NaCl, 0.5% NP40, 0.1 mM EDTA and 10% Glycerol) supplemented with complete protease and phosphatase inhibitors (Roche Applied Biosciences). Cell lysate concentrations were measured by Bradford assay (Biorad) followed by SDS-PAGE analysis with equal amount of lysates supplemented with 3xSDS loading dye. Rabbit EglN2 antibody (NB100-310) was from Novus Biological. Rabbit anti Cyclin D1 (RB-010-P1) was from Neomarker. Antibodies against Vinculin (V9131), Tubulin (T9026) and FLAG (A8592) were from Sigma. Cyclin E1 (SC-247), c-Myc (SC-40), GFP (SC-9996) antibodies were from Santa Cruz. c-Jun (9165), p27 (3688) and EglN1 (3293S) antibodies were from Cell Signaling. HIF1α antibody (610959) was obtained from BD Bioscience. Mouse antibody against hemagglutinin (HA, MMS-101P) was obtained from Covance. Mouse Peroxidase conjugated goat anti-mouse secondary antibody (31430) and peroxidase conjugated goat anti-rabbit secondary antibody (31460) were purchased from Thermo Scientific.
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