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11 protocols using alexa fluor 546 goat anti rat igg

1

Immunofluorescence Imaging of C. elegans Embryos

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Embryos obtained from dissected gravid adult hermaphrodites or synchronized L1-stage larvae were placed on poly-lysine-coated glass slides, freeze-cracked with liquid nitrogen, fixed with cold methanol and cold acetone, and immunostained with primary and secondary antibodies as previously described5 (link)6 (link)8 (link). The following primary and secondary antibodies were used: rabbit anti-PGL-1 antibody5 (link) (1:4,000), rabbit anti-GFP antibody (1:400; Molecular Probes), mouse monoclonal OIC1D4 antibody that specifically recognizes PGL-1 (undiluted; Developmental Studies Hybridoma Bank), rat anti-PGL-3 antibody6 (link) (1:1,000), rabbit anti-SIR-2.1 antibody (1:500; Novus), Alexa Fluor 488 goat anti-rabbit IgG (1:500; Molecular Probes), Alexa Fluor 546 goat anti-mouse IgG (1:500; Molecular Probes), and Alexa Fluor 546 goat anti-rat IgG (1:500; Molecular Probes). The specimens were further counter stained with 1 μM TO-PRO-3 (Molecular Probes) to stain DNA. Immunofluorescence images were acquired using a confocal microscope (Olympus, FV1000 Spectral).
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2

Immunostaining of mouse lung cells

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Mouse lung cells were fixed, blocked and permeabilized with BD Cytofix/Cytoperm Kit, according to the manufacturer’s instructions. Cells were then incubated with goat anti‐mouse pro‐surfactant protein C) (proSP‐C; Santa Cruz Biotechnology, Dallas, TX, USA) or rat anti‐(mouse CD31) (BD Pharmingen) IgG at 4 °C overnight and then incubated for 1 h with Alexa Fluor 546 donkey anti‐(goat IgG) or Alexa Fluor 546 goat anti‐(rat IgG) (Molecular Probes, Carlsbad, CA, USA), respectively.
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3

Evaluating Retinal Hypoxia in Mice

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Tissue hypoxia in mouse retinas was evaluated using the Hypoxyprobe Plus Kit (Hypoxyprobe, Burlington, MA). Pimonidazole hydrochloride was administered intraperitoneally to mice at a dosage of 60 mg/kg body weight. The mice were euthanized 40 minutes after the injection of pimonidazole hydrochloride, and retinal flat mounts were prepared. After the fixation in 4% paraformaldehyde (PFA), retinal flat mounts were incubated with both the FITC conjugated mouse anti-pimonidazole monoclonal antibody (1/100 dilution) and the rat monoclonal antibody against CD31 (PECAM-1) (1/100 dilution; BD Biosciences, San Jose, CA) at 4 °C overnight, and subsequently reacted with Alexa Fluor 546 goat anti-rat IgG (1/200 dilution; Molecular Probes) at room temperature for 3 hours. An antibody against CD31 was used to visualize retinal vasculature by staining of endothelial cells. The stained flat mounts were observed with a Zeiss LSM 510 META laser confocal microscope Carl Zeiss.
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4

Immunohistochemical Characterization of Cells

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The cells were fixed with 4% paraformaldehyde for 15 min at room temperature. Fixed cultures were washed with PBS, permeabilized with 0.2% Triton X-100 in PBS for 3 min, and blocked for 1 h with 5% bovine serum albumin (BSA). Next, the cells were incubated with anti-BrdU (Sigma, 1:500), polyclonal anti-fibronectin (Sigma, 1:400) and anti-laminin (Sigma, 1:50), anti-Sox2 (Millipore, 1:100), anti-CD133 (Millipore, 1:20) antibodies or double-stained with polyclonal anti-GFAP (DAKP, 1:500) and monoclonal anti-Nestin (BD Biosciences 1:50) antibodies overnight at 4°C. Incubation with specific secondary Alexa Fluor 546 goat anti-mouse IgG (Molecular Probes 1:800), Alexa Fluor 488 goat anti-rabbit (Molecular Probes 1:400) or Alexa Fluor 546 goat anti-rat IgG (Molecular Probes 1:500) proceeded for 1 h at room temperature. Then, the cells were washed with PBS, stained with DAPI (Sigma), washed again and mounted. For negative controls, cells received similar treatment but the primary antibodies were omitted. The slides were observed in a Nikon TE 2000 inverted microscope. Images were captured using a CoolSNAP-Pro (Media Cybernetics) digital camera.
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5

Antibody Validation for Cell Signaling Studies

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Commercially available antibodies used for IP, immunoblotting, and immunofluorescence were as follows: Goat anti–apolipoprotein B (EMD, Hayward, CA; #178467 1:500 for immunoblot); rabbit anti-FABP5 human (Proteintech, Rosemont, IL; #12348-1-AP 1:2000 for immunoblot); rat anti-FABP5 monoclonal antibody (Thermo Fisher Scientific, Waltham, MA; ma5-24029 1:300 for immunofluorescence); rabbit anti–PC1 LF-41 was a gift from L. Fisher (National Institute of Dental and Craniofacial Research, Bethesda, MD [Fisher et al., 1989 , 1995 (link); Bernstein et al., 1996 (link)]; 1:5000 for immunoblot); rabbit anti-collagen type I (Millipore, Hayward, CA; #AB745 1:300 for immunofluorescence); Alexa Fluor 488 donkey anti-rabbit immunoglobulin G (IgG) (Invitrogen, Carlsbad, CA; #A-21206 1:250 for immunofluorescence); Alexa Fluor 546 goat anti-rat IgG (Invitrogen #A-11081 1:250 for immunofluorescence).
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6

Immunofluorescence Microscopy of Cytoskeletal Proteins

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The following antibodies were used: mouse anti–acetylated tubulin (clone 6-11B-1; T6793; Sigma-Aldrich), mouse anti–α-tubulin (clone B-5-1-2; T5168; Sigma-Aldrich), monoclonal rabbit anti–α-tubulin (clone EP1332Y; 04–1117; EMD Millipore), monoclonal rat anti–tyrosinated α-tubulin (gift of A. Andrieux, Grenoble Institut des Neurosciences, Grenoble, France), rabbit anti–kinesin heavy chain (AKINO1; Cytoskeleton, Inc.), mouse anti–dynein intermediate chain (clone 74.1; MAB1618; EMD Millipore), nonimmune rabbit IgGs (I5006; Sigma-Aldrich), Alexa Fluor 488 goat anti–mouse IgG (A11029; Invitrogen), Alexa Fluor 488 goat anti–rabbit IgG (A11034; Invitrogen), Alexa Fluor 546 goat anti–mouse IgG (A11030; Invitrogen), Alexa Fluor 546 goat anti–rabbit IgG (A11035; Invitrogen), Alexa Fluor 546 goat anti–rat IgG (A11081; Invitrogen), Alexa Fluor 647 goat anti–rabbit IgG (A21245; Invitrogen), HRP goat anti–rabbit IgG (P0448; Dako), and HRP goat anti–mouse IgG (P0447; Dako). The following reagents were used: phalloidin-rhodamine (Sigma-Aldrich), Tubulin Tracker (Invitrogen), cytochalasin D (Sigma-Aldrich), poly-d-lysine (Sigma-Aldrich), thrombin (Sigma-Aldrich), arachidonic acid (Helena Biosciences), and ADP (Helena Biosciences).
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7

Immunofluorescent Staining of Foxp3, CCL1, CCR8

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The tissues were incubated with antibody against Foxp3, CCL1, CCR8 (abcam) at 1:100 dilutions at 4°C for overnight, followed by incubation with Alexa Fluor 488 goat anti-rabbit IgG, Alexa Fluor 594 goat anti-rabbit IgG and Alexa Fluor 546 goat anti-rat IgG (Invitrogen Inc.) at room temperature for 1 hour, then counterstained with DAPI for 2 minutes and subjected to image with a confocal microscope (Olympus).
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8

Quantifying Vascular and Immune Responses in Tooth Extraction Sockets

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To detect blood vessels and macrophages in the connective tissue of tooth extraction sockets, rat anti-mouse CD31 monoclonal antibody (ab56299; Abcam, Cambridge, MA; 1:100 dilution), rat anti-mouse F4/80 monoclonal antibody (ab16911; Abcam; 1:50 dilution), and rabbit anti-mouse CD206 polyclonal antibody (ab64693; Abcam; 1:50 dilution) were used as primary antibodies. Alexa Fluor 488 goat anti-rabbit IgG and Alexa Fluor 546 goat anti-rat IgG (Invitrogen, Carlsbad, CA; 1:200 dilution) were used as secondary antibodies. Sections were mounted with VECTASHIELD Antifade Mounting Medium with DAPI (H-1200; Vector Laboratories, Burlingame, CA). Stained sections were photomicrographed by fluorescence microscopy (Axio Scope A1; Zeiss) and were histomorphometrically analyzed with ZEN2 software and NIH ImageJ to yield the following parameters: the number of blood vessels [blood vessels (#/mm2)]; vessel surface area in the AOIs of soft tissue in the tooth extraction sockets [vessel density (%)] (AOI, 200 × 1000 μm); F4/80+CD206 macrophages [F4/80+CD206 cells]; and F4/80+CD206+ macrophages [F4/80+CD206+ cells] in the AOIs of soft tissue in the extraction sockets (AOI, 200 × 1000 μm).
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9

Immunofluorescence Analysis of Ki67 in Skin Biopsies

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For immunofluorescence analyses skin biopsies were frozen in Tissue-Tek embedding medium (Sakura, Zoeterwonde, Netherlands). 14 μm cryosections were fixed in 4% paraformaldehyde for 5 min, washed 3 times in TBS-TX (50 mM Tris, 1.5% NaCl, 0.3% TritonX-100) and blocked for 1 h with 4% bovine serum albumin and 1% normal goat serum in TBS-TX. Primary rat anti-Ki67 antibody (monoclonal, diluted 1:50, DakoCytomation, Glostrup Denmark, Cat. No. M7249) was diluted in blocking solution and incubated with cryosection over night at 4 °C. Afterwards the sections were washed 3 times with TBS-TX and incubated with secondary antibodies Alexa Fluor 546 goat anti-rat IgG (diluted 1:1000, Invitrogen, Cat. No. A-11081, USA) for 45 min. Then the stained sections were washed 3 times with TBS-TX, embedded in Glycergel mounting medium (DakoCytomation), and analyzed by confocal microscopy (Zeiss, LSM 710, Germany).
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10

Immunofluorescence Analysis of Tumor Hypoxia

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Immunofluorescence detection of hypoxic regions was performed as previously
described (22 ). Briefly, SCID mice bearing
3-week-old orthotopic MGG123 xenografts were given intraperitoneal injection of 60 mg/kg
Hypoxyprobe (pimonidazole hydrochloride). One hour later mice were euthanized,
cardiac-perfused with 4% paraformaldehyde, the brains removed, and frozen sections
obtained. Slides were stained with anti-Hypoxyprobe (1:50) and anti-CD34 (Abcam, 1: 100),
followed by incubation with Alexa Fluor 488 goat anti-mouse IgG and Alexa Fluor 546 goat
anti-rat IgG (both from Invitrogen). Slides were then mounted with DAPI-containing media
(Vector Laboratories) before microscopic observation. Images were captured using SPOT
imaging software.
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