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15 protocols using f9887

1

Immunofluorescence Staining for NSE, GFAP, Iba-1, and MT-CO1

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Immunofluorescence staining for NSE was mouse γ enolase (NSE-P1) monoclonal antibody (1:500; sc-21738, SANTA CRUZ); immunofluorescence staining with rabbit polyclonal GFAP antibody (with ratio either 1:200 or 1:400; GTX108711, and GTX27260 GeneTex) was performed to assess astrogliosis. Immunofluorescence staining with rabbit polyclonal Iba-1, (product full name with allograft inflammatory factor 1, synonyms as ionized calcium-binding adapter molecule 1 antibody) antibody (1:200, GTX101495, GeneTex) was performed to assess microgliosis. The secondary antibody for GFAP and Iba-1 was anti-rabbit IgG-fluorescein isothiocyanate (FITC) antibody produced in goat (1:600; F9887, Sigma–Aldrich). Immunofluorescence staining of MT-CO1 was performed using rabbit monoclonal anti-MT-CO1 antibody (1:1000; ab203917, Abcam) following Purushothuman et al.28 (link) and the secondary antibody was Cy3-AffiniPure donkey anti-mouse IgG (H+L; 715-165-151, Jackson ImmunoResearch).
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2

Immunofluorescence Staining of Nestin, Vimentin, and PCNA

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EC were fixed using 4% paraformaldehyde solution in PBS, permeabilised in 0.5% triton X-100 and then blocked using 5% BSA. Primary antibody against nestin (HPA007007, Atlas Antibodies), Vimentin (OMA1-06001, Invitrogen) or PCNA (LifeSpan Biosciences), was incubated with the cells for 20 minutes, followed by FITC-conjugated anti-rabbit antibody (F-9887, Sigma), or Alexa-Fluor 647 conjugated anti-mouse antibody (A-21235, Invitrogen). Some experiments were also actin-stained with TRITC-conjugated phalloidin (P1951, Sigma). Cells were covered with 40 μl DAPI-containing mounting medium (Vectashield) before imaging. Fluorescence images were taken using a Leica TPS SP5 confocal microscope, and were processed using Fiji image processing software98 (link). For measurement of percentage of nestin coverage, between 10–30 cells per image were individually selected and outlines saved as separate overlays using selection tools and the Region of Interest (ROI) manager, and coverage determined using the default threshold tool. Cell area was determined using actin staining and a high contrast filter/look up table. Co-localisation was calculated for each individual cell using the Coloc2 plugin.
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3

Immunofluorescent Localization of USF1 in Oocytes and Embryos

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Immunofluorescent staining was performed for USF1 protein localization in oocytes and embryos according to previously published protocols (Tripurani et al. 2011 (link)). After fixation, permeabilization and blocking, samples were probed with commercially available rabbit polyclonal anti-USF1 antibody [1:200 (v/v), Santa Cruz Biotechnology, sc229] and corresponding fluorescein isothiocyanate-conjugated secondary antibody [0.5% (w/v) F9887; Sigma-Aldrich, St. Louis, MO]. Immunostaining experiments were replicated four times using at least 10–12 oocytes/embryos per sample. Oocytes and embryos incubated without the primary USF1 antibodies were used as negative controls.
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4

Detecting E-cadherin Expression in GES-1 Cells

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Immunofluorescence assays were used to detect the expression of E-cadherin in GES-1 cells cultured with the CM of macrophage-hucMSCs (28 (link)). GES-1 cells cultured with the CM of macrophage-hucMSCs in 24-well plates for 48 h were washed three times with PBS, fixed with 4% paraformaldehyde at room temperature for 20 min, permeabilized with 0.1% Triton X-100 for 5 min, blocked with 5% bovine serum albumin (Boster Biological Technology, Pleasanton, CA, USA) at room temperature for 30 min, and then incubated with anti-E-cadherin antibodies at a dilution of 1:100 (cat. no. BS1098; Bioworld Technology, Inc.) at 4°C overnight, followed by incubation with a fluorescein isothiocyanate (FITC)-conjugated anti-rabbit secondary antibody at dilution of 1:200 (F9887; Sigma-Aldrich; Merck KGaA) at 37°C for 1 h. The cells were then stained with DAPI (Beyotime Institute of Biotechnology) for nuclear staining. Images were then acquired with a Nikon TE300 Inverted Fluorescence Phase Contrast Microscope (Nikon Corporation, Tokyo, Japan), magnification, ×200.
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5

Quantifying SARS-CoV-2 Spike Protein Expression

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After collecting virus from the 293T cells used to produce the lentiviral vectors, the producer cells were washed in PBS and detached using PBS + 5 mM EDTA. A portion of these cells were taken and fixed using 3.7% formaldehyde for 10 min at room temperature. Cells were stained with polyclonal anti-S1 antibody (Sino Biological, 40591-T62; RRID: AB_2893171) for 1.5 h and washed three times with PBS + 2% FBS. The secondary stain used was anti-Rabbit-IgG-FITC (Sigma, F9887, RRID: AB_259816). Cells were then washed another 3 times then flow cytometry was performed using a LifeTechnologies Attune NxT flow cytometer. Data analysis was conducted using FlowJo v10.9.1 (Ashland, OR).
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6

SARS-CoV-2 S1 Antibody Staining

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A portion of 293T cells used to produce the lentiviral vectors were collected by detaching with PBS + 5Mm EDTA and fixed in 3.7% formaldehyde for 10 minutes and room temperature. Cells were then stained with polyclonal anti-SARS-CoV-2 S1 antibody (Sino Biological, 40591-T62; RRID: AB_2893171) followed by anti-Rabbit-IgG-FITC (Sigma, F9887, RRID: AB_259816) secondary to visualize on a Life Technologies Attune NxT flow cytometer. FlowJo v10 (Ashland, OR) is used to analyze data.
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7

Immunolocalization of CYP405A2 in Larval Tissues

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Immunolocalization was performed on 100 µm sections prepared on a vibratome (Leica VT 1000S) from second to third instar larvae reared on (+)diet in order to determine the localization of CYP405A2. Larvae of later instars could not be sectioned using this method. CYP405A2 was detected using polyclonal antibodies against CYP405A2 (dilution 1∶100, Figure S2) as primary antibodies and anti-rabbit IgG antibody produced in goat with fluorescein isothiocyanate (FITC) attached (dilution 1∶160) as secondary antibody (F9887; Sigma-Aldrich, MO, US) according to [64] (link). The localization of CYP405A2 was visualized using fluorescence microscopy (Leica DMR HC, filter N2.1, λex BP 515–560 and λem LP 590).
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8

Quantitative Analysis of Apoptosis in Mice Brain

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Mice were anesthetized with isoflurane and then perfused with 50 mL of normal saline through the left ventricle followed by a 50 mL 4% paraformaldehyde solution after decompression. The brain tissue was removed quickly and then post-fixed for 48 hours in 4% paraformaldehyde solution. The brains were serially cut into 25 μm-thick coronal sections from the same region, and then diaminobenzidine (DAB) staining was performed. In brief, sections were incubated at 4°C overnight with rabbit anti-cleaved caspase-3 polyclonal antibody (1:1000; #9662; CST Co., Boston, USA), followed by incubation with a secondary antibody (Goat anti-Rabbit, 1:200, F9887, Sigma-Aldrich Co., St. Louis, Missouri, USA) for one hour; the sections were then incubated with DAB (D5637, Sigma-Aldrich Co., St. Louis, Missouri, USA) solution until brown products appeared under the microscope. Finally, the sections were examined under a microscope (DM 4000B, Leica, Wetzlar, Hesse-Darmstadt, Germany), and then quantitated as the percentage (caspase-3 positive cells / Nissl positive cells) with Image-pro Plus 5.1 software (Media Cybernetics, Bethesda, Maryland, USA).
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9

Immunofluorescence Staining of Cells and Tissues

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After treatment, the samples (cells cultured on glass coverslips and frozen mouse skin sections) were fixed in 4% paraformaldehyde for 20 min. The samples were incubated with primary antibodies at 4°C overnight and washed three times with phosphate-buffered saline (PBS). Next, the samples were stained with fluorescent secondary antibodies for 1 h at 37°C. Primary antibodies against the following were used: vimentin (10366-1-AP, 1 : 200, Proteintech), E-cadherin (20874-1-AP, 1 : 200, Proteintech), N-cadherin (22018-1-AP, 1 : 200, Proteintech), SOX2 (ab79351, 1 : 100, Abcam), and Slug (#9585, 1 : 1000, CST). The following secondary antibodies were used: FITC-labelled goat anti-rabbit IgG (F9887, 1 : 500, Sigma) and DyLight 594-labelled goat anti-mouse IgG (ab96881, 1 : 500, Abcam). The nuclei were then counterstained with DAPI (Abcam) before imaging. IF images were captured using fluorescence microscopy (Leica Microsystems, Germany).
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10

Porcine Cornea Infection and Immunostaining

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Porcine corneas were obtained and handled as described above. After excising and 1 h incubation in cornea media, each half cornea was infected with 106 pfu of strain 17 or 17Δγ34.5 mutant virus in 1 mL of media. At 48 hpi, corneas were washed in PBS and embedded in Tissue-Tek OCT compound (Sakura Finetek, Torrance, CA) and stored at −80°C. 10 μm sections were cut using Cryostar NX50 microtome (Thermo Scientific). Sections were air dried at room temperature for 10 min and then fixed in ice-cold acetone for 15 min. Two 10 min washing steps were performed in TBS containing 0.05% Tween 20 (TBS-T) before blocking with 1% BSA in TBS-T for 1 h at room temperature. Sections were then incubated with a cocktail of mouse anti-HPSE (1:100, Santa Cruz Biotechnology sc-293205) and rabbit anti-HSV (1:100, Abcam ab9533) overnight at 4°C. As a control, sections were incubated without primary antibodies. After subsequent washes in TBS-T sections were incubated with a cocktail of anti-mouse Cy5 (1:200, Abcam ab6563) and anti-rabbit FITC (1:200, Sigma F9887) for 1 h at room temperature. Following washes in TBS-T, sections were mounted in Vectashield mounting media containing DAPI (Vector Laboratories, Burlingame, CA) and imaged at 20× magnificiation on LSM 710 confocal microscope (Zeiss).
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