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103 protocols using a6455

1

Immunostaining Analysis of Mammalian Expression Vectors

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Mammalian (pCaggs) expression vectors encoding p27kip1, p27kip1(ck-) and RhoA(N19) have been described previously [16 (link)], while an Rp58 expression construct with a pCIG vector which lacks a GFP cassette was used [11 ]. RNAi for Rp58 was achieved using a pool of targeting siRNAs (Dharmacon GE Life Sciences) which was previously verified for specificity of knockdown as well as a pSilCaggs-Rnd2shRNA1 vector to induce Rnd2 RNAi [11 ]. Primary antibodies used for immunostaining analysis include chicken antibody to GFP (Abcam, ab13970, 1:700), mouse anti-p27kip1 (BD Biosciences, 1:400), rabbit anti-Rp58 (Proteintech Group, 1:250), rabbit anti-Ki67 (NCL-Ki67p, Leica, 1:1000), pHH3(ser10) (06–570, Merck Millipore, 1:1000), mouse anti βIII-tubulin (Covance, MMS-435P, 1:1000), mouse anti-Nestin (Millipore, MAB353, 1:300), rabbit anti-Pax6 (Covance, PRB-2788, 1:500), rabbit anti-Tbr2 antibody (Abcam, ab233345, 1:500), rabbit polyclonal antibody to GFP (Invitrogen, A6455, 1:1000). Alexa fluor secondary antibodies include goat anti- chicken IgG (Invitrogen, A11039, 1:700), goat anti-mouse (Invitrogen, A11031, 1:800), and goat anti-rabbit IgG (Invitrogen, A6455, 1:1000). The nuclei of cells were visualised with DAPI.
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2

Immunofluorescence Labeling of Drosophila Brains

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Immunofluorescence studies were performed as follows60 : 5–6 day old larvae were dissected in phosphate buffer saline (PBS) or HL3.1 (pH 7.2)61 (link), fixated in 4% paraformaldehyde in PBS for 40 min, washed in PBS with 0.3% Triton-X 100 (PBT), and afterwards blocked in 5% normal goat serum in PBT. Specimens were incubated in primary antibody solution containing polyclonal rabbit anti-GFP antibody (A6455, Molecular Probes, dilution 1:1000) or monoclonal mouse anti-GFP (A11120, Molecular Probes, dilution 1:250), polyclonal rabbit anti-sNPFp (ref. 40 (link), dilution 1:1000) and 3% normal goat serum in PBT for one to two nights at 4 °C. Then brains were washed six times in PBT and incubated for one night at 4 °C in secondary antibody solution containing goat anti-rabbit Alexa 488 (Molecular Probes, dilution 1:250) or combined goat anti-mouse DyLight 488 (Jackson ImmunoResearch, dilution 1:250) and goat anti-rabbit Alexa 635 (Molecular Probes, dilution 1:250). Finally, specimens were rinsed six times in PBT and mounted in 80% glycerol or Vectashield mounting medium (Vector Laboratories, USA). Until scanning with a Leica SP8 confocal light scanning microscope, brains were stored in darkness at 4 °C. Image processing was performed with Fiji62 (link) and Adobe Photoshop CS6 (Adobe Systems, USA).
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3

Immunostaining of Drosophila Brain

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To analyze the expression pattern of OK107-Gal4 rabbit anti-GFP antibody (A6455, Molecular Probes; 1:1000) and two different mouse antibodies for staining the cholinergic neuropil (ChAT4B1; DSHB, Iowa City, IA, 1:150) and axonal tracts (1d4 anti-Fasciclin 2; DSHB, Iowa City, IA; 1:50) were applied [71 (link), 117 ]. A specific antibody for the Synapsin protein was used to verify the mutation syn97 (monoclonal mouse anti-syn, 3C11; DSHB, Iowa City, IA, 1:10) [54 (link)]. To analyze if the expression level of Bruchpilot is specifically reduced in the MB KCs by driving UAS-RNAiB3C8 via OK107-Gal4, monoclonal mouse anti-nc82 was used (nc82, DSHB, Iowa City, IA, 1:10) [58 (link)]. As secondary antibodies goat anti-rabbit IgG Alexa Fluor 488 (A11008, Molecular Probes, 1:200) and goat anti-mouse IgG Alexa Fluor 647 (A21235, Molecular Probes, 1:200) were used.
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4

Visualizing Neuronal Populations in Drosophila

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Anti-GFP (polyclonal/rabbit/A6455/Molecular Probes/1:1000), Anti-GFP-FITC (polyclonal/goat/ ab6662/abcam/1:1000) and anti-DsRed (polyclonal/rabbit/632496/Clonetech/1:200) were used for visualizing Gal4 lines expression patterns. Two different mouse antibodies for staining the neuropil (anti-ChAT (monoclonal/mouse/ChAT4B1/DSHB/1:100)) and the axonal tracts (anti-Fasciclin II (monoclonal/1d4 anti-Fas/DSHB/1:50)) were applied to provide landmarks within the larval CNS. 5-HT cells were visualized with anti-5-HT (polyclonal/rabbit/S5545/Sigma Aldrich /1:1000), dopaminergic cells with anti-TH (monoclonal/mouse/22941/Immuno-Star/1:500), respectively.
As secondary antibodies goat anti-rabbit IgG Alexa Fluor 488 (polyclonal/A11008/Molecular Probes/ 1:200), goat anti-mouse IgG Alexa Fluor 647 (polyclonal/A21235/Molecular Probes/1:200), goat anti-mouse IgG Alexa Fluor 405 (polyclonal/A31553/Molecular Probes/1:200), goat anti-mouse IgG Cy3 (polyclonal/A10521/Molecular Probes/1:200), and goat anti-rabbit IgG Cy5 (polyclonal/A10523/Molecular Probes/1:200) were used.
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5

Antibodies for Protein Localization and Detection

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Antibodies against Sec61 were as described (132 (link)). H. D. Schmitt provided anti-Emp47 antibodies. We derived monoclonal anti-HA antibodies from hybridoma cells (12CH5). We purchased anti-PGK (A6457, Molecular Probes), anti-GST (600-101-200, Rockland), polyclonal anti-GFP for immunoprecipitation (A6455, Molecular Probes), monoclonal anti-GFP for immunodetection (JL-8, Clontech), anti-Myc (M5546, Sigma–Aldrich), anti-FLAG (M2, F3165, Sigma–Aldrich), and anti-GAPDH (MAB374, Sigma–Aldrich). Horseradish peroxidase–coupled secondary antibodies (Sigma–Aldrich) were used to visualize immunoblots by Western Lightning Plus ECL (PerkinElmer Life Sciences) and autoradiography films (X-Omat, Kodak). For immunogold labelings, a rabbit anti-GFP antibody (Abcam, ab6556; diluted 1:100) and a 12-nm colloidal gold goat anti-rabbit secondary antibody (Dianova, 111-205-144; diluted 1:30) were used.
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6

Antibodies for Chlamydia trachomatis study

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Polyclonal antibodies against C. trachomatis HtrA were generated previously (Huston et al., 2008 (link)). Monoclonal antibodies against EEA1 (610457, 1:100), SNX1 (611483,1:200) and SNX2 (611308, 1:200) were supplied by BD Bioscience. Monoclonal antibodies against the myc epiptope (9B11, 1:2000) were supplied by Abcam. Rabbit polyclonal antibodies against GFP (A-6455, 1:500) were purchased from Molecular Probes (Invitrogen). Rabbit polyclonal antibodies against Rab5 (C8B1, 1:100) were from Cell Signaling Technology. Goat polyclonal antibodies against Vps35 (IMG-3575, 1:400) were from Imgenex. Secondary antibodies were purchased from Molecular Probes (Life Technologies) and Li-Cor Bioscience. Wortmannin was supplied by Sigma-Aldrich (W1628). VPS34-In1 was from Merck Millipore (532628).
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7

ABC Protein Localization Protocol

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Protoplasts expressing ABC-GFP, ABC1–4-GFP, and ABC1–5-GFP were immunolabeled with anti-GFP serum (A6455, Molecular Probes, http://www.invitrogen.com/) and Alexa Fluor 546-conjugated anti-rabbit IgGs (Molecular Probes) as reported in De Caroli et al. (2011a (link)).
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8

Chemerin and GFP Protein Detection

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Tissues were lysed by incubation for 5 min at 94°C in 62.5 mM Tris-HCl pH 6.8 containing 3% SDS, and insoluble material removed by centrifugation at 15,000 g for 5 min. The protein concentration was measured by using the bicinchoninic acid (BCA) assay kit (Pierce Thermo Scientific) and the extract adjusted to 62.5 mM Tris-HCl pH 6.8, 5% β-mercaptoethanol, 3% SDS, 10% glycerol and 0.01% bromophenol blue. Protein lysates (10 μg proteins per sample) were separated on 15% SDS-PAGE gels and transferred onto nitrocellulose membranes. The membranes were incubated in blocking buffer (PBS containing 5% BSA and 0.1% Tween 20) for 1 h at room temperature, then probed overnight at 4°C with goat anti-chemerin (R&D Systems, AF2325, RRID:AB_2175558, 1/250) and rabbit anti-GFP (Molecular Probes, A6455, RRID:AB_221570, 1/2000) antibodies diluted in PBS containing 3% BSA and 0.1% Tween 20. Membranes were washed three times in PBS containing 0.1% Tween 20, then probed with HRP-conjugated anti-rabbit or anti-goat antibodies (Thermo Fisher Scientific, 31460, RRID:AB_228341 and 31402, RRID:AB_228395, 1:50,000 in the same buffer) for 1 h at room temperature. Proteins were visualized by enhanced chemiluminescence using the SuperSignal West Pico HRP substrate (Pierce Thermo Scientific).
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9

Antibodies for Cytoskeletal Analysis

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The following antibodies were used: NMIIA for Western blot and immunofluorescence (rabbit pAb PRB-440P; Covance), NMIIB for Western blot (rabbit pAb PRB-445P; Covance), NMIIB for immunofluorescence (mouse mAb ab684; Abcam), GAPDH (rabbit pAb sc-25778; Santa Cruz Biotechnology, Inc.), and GFP (rabbit pAb A6455; Molecular Probes). DAPI and Alexa Fluor 647 Phalloidin were purchased from Life Technologies (D3571 and A22287, respectively) and used according to the manufacturer’s recommendation. Nesprin-1 and -2 antibodies were obtained from MDA Monoclonal Antibody Resource (mouse mAb; MANNES1E and MANNES2G, respectively).
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10

Immunoblotting Antibody Optimization

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Primary antibodies: anti-β-actin (1:16,000; A5441, Sigma), anti-EMMPRIN (1:1000; AF972-SP, R&D Systems), anti-GAPDH (1:6000; NB300-221, Novus Biologicals), anti-GFP mouse monoclonal (1:4000; 66002-1-lg, Proteintech), anti-GFP rabbit polyclonal (1:32,000; A6455, Molecular Probes), and anti-pan-cadherin (1:1000; 4068, Cell Signaling Technology). Secondary antibodies: horseradish peroxidase (HRP)-conjugated AffiniPure anti-rabbit immunoglobulin G (IgG, 711-035-152), HRP-conjugated AffiniPure anti-mouse IgG (715-035-150), and HRP-conjugated AffiniPure anti-goat IgG (705-035-003). All secondary antibodies were used at 1:8000 and obtained from Jackson ImmunoResearch.
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