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48 protocols using cm 3000

1

Immunofluorescence Detection of NF-κB in MGC-803 Cells

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MGC-803 cells were cultured on six-well chamber slides and fixed with 4% paraformaldehyde for 10 min at −20°C. The slides were washed in PBS three times and incubated with a polyclonal antibody against NF-κB (1:50 diluted in PBS with 1% BSA; 50 μl/slide) for 2 h at room temperature. After washing with PBS three times (5 min per time), the slides were incubated with tetramethylrhodamine-conjugated anti-rabbit IgG (Beijing Zhongshan Jinqiao Biotechnology Co., Ltd, Beijing, China; diluted 1:100 in PBS with 1% BSA; 50 μl/slide) for 1 h at room temperature. Three times after washing the slides in PBS, the slides were incubated with Hoechst 33258 (10 μg/ml) for 5 min. The slides were then washed again and examined using a fluorescence microscope (Leica CM3000; Leica Microsystems GmbH, Buffalo Grove, IL, USA).
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2

Immunofluorescent Localization of HuR Protein

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The HL60 cells were cultured in 6-well chamber slides and fixed with 4% paraformaldehyde at a density of 1×105 cells/well for 10 min at −20°C. The slides were washed three times in PBS and incubated with a polyclonal antibody targeting HuR (cat. no. 12582) diluted in PBS (1:50) supplemented with 1% bovine serum albumin (BSA; Sigma-Aldrich) at 50 µl/slide for 2 h at room temperature. Following three washes with PBS (5 min each), the slides were incubated with tetramethylrhodamine-conjugated anti-rabbit IgG (1:100; cat. no. AP132R; Chemicon, Temecula, CA, USA). diluted in PBS (1:100) supplemented with 1% BSA at 50 µl/slide, for 1 h at room temperature. Following three washes with PBS, the slides were incubated with 10 µg/ml Hoechst 33258 for 5 min. The slides were washed again and examined using a fluorescence microscope (Leica CM3000; Leica Microsystems GmbH, Wetzlar, Germany).
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Immunohistochemical Analysis of Mouse Brain

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Mice were anesthetized with sevoflurane and perfused with PBS (phosphate buffered saline). After perfusion, the left hemisphere of the mouse brains was dissected and the right hemisphere brain was fixed with 4% PFA for one day [28 (link)]. The frozen brains were sectioned in a coronal manner (30 μm thick) using a cryostat (Leica CM3000, Leica Microsystems, Germany). Sections were stored in a deep freezer (-70°C) until immunohistochemical analysis. In all immunofluorescence labeling procedures, we rinsed off the brain sections and blocked the tissues with cold PBST (0.1% Triton X-100 in PBS) containing 5% BSA and 5% goat serum at room temperature. We incubated them with primary antibodies, including mouse anti-6E10 antibody (1:3000, Covance, USA), rabbit anti-GFAP antibody (1:4000, Dako, Germany), and rabbit anti- Iba1 antibody (1:3000, Wako, USA), diluted in PBS. After the first incubation step, the brain sections were washed thrice with PBS for 10 min each, and incubation with secondary antibodies followed. For secondary antibodies, goat Alexa Fluor® 488 conjugated anti-rabbit antibody and goat Alexa Fluor® 568 anti-mouse antibody (Invitrogen, USA) were prepared at a dilution of 1:2000 in PBS.
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4

Visualizing Liver Uptake of Labeled siRNA Using MEND Delivery

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Optimized MENDs encapsulating Cy5-labeled siRNA were administered into male ICR mice (5–6 weeks old). Five min before projected sacrifice, FITC-conjugated isolectin B4 (40 μg/mouse) was intravenously injected via the tail vein to stain blood vessels. At 30 min after intravenously injection of optimized MEND, each animal was perfused with PBS to remove blood from the liver, then with 4% paraformaldehyde (PFA)-PBS for fixation. Liver tissues were excised and further fixed with 4% PFA-PBS for 24 hr at 4°C, then submerged in 20% sucrose-PBS for 4 hr at 4°C. The liver was embedded in OCT compound (Sakura Fine Technical, Tokyo, Japan) and snap-frozen in liquid nitrogen. Frozen samples were cut in 30 μm-thick sections (LEICA CM3000, Leica Microsystems, Wetzlar, Germany). The samples were stained with Hoechst33342 to detect nuclear DNA, and observed at an excitation wavelength of 633 nm using a laser-equipped Nikon A1 (Nikon Co. Ltd., Tokyo, Japan) with a x60 objective lens.
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5

Scleral Thickness and Histological Evaluation

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The eyes were enucleated, and the part of the sclera with the sclerotomy site was removed and evaluated under slit-lamp biomicroscopy (Topcon SL-D7) through pictures. Then, the scleral thickness was measured using a digital caliper (Mitutoyo, Kawasaki, Japan; Figure 1B). Next, it was placed in a 4% paraformaldehyde solution for 2 hours. After that, the tissue was placed in a graded sucrose solution series (10, 20, and 30%) for 24 hours. At the end, the sclera was placed in aluminum chambers filled with optimum cutting temperature solution (Tissue-Tek, Delaware, PA, USA). Frozen sections were prepared using Cryostat (Leica CM 3000; Leica Microsystems, Wetzlar, Germany) with 10 μm slices performed until the sclerotomy site was found. Parts of the tissue slices were stained with hematoxylin–eosin (HE) and the other part with picrosirius red (PR).
The specimens stained with the routine HE were evaluated under optical microscope (Carl Zeiss Meditec AG, Jena, Germany) to evaluate cellularity.
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Immunohistochemistry of Rat Brain Tissue

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Immunohistochemistry (IHC) was performed as previously described in Ippolito and Eroglu (2010) with modifications. Briefly, rats were deeply anesthetized with isoflurane and transcardially perfused with phosphate buffered saline (PBS), pH 7.4, containing 25 U/ml heparin, followed by 4% paraformaldehyde in PBS. Brains were removed and post-fixed for 24 hrs at 4°C in 4% paraformaldehyde in PBS. The brains were rinsed in PBS and placed in 30% sucrose in PBS. Upon sinking, brains were removed and frozen in tissue freezing medium (Electron Microscopy Sciences, Hatfield, PA, USA) and stored at −80°C. Sagittal sections (20µm) were cut using the Leica CM 3000 (Leica Microsystems, Buffalo Grove, IL, USA) and placed in glycerol:tris buffered saline solution. When necessary, adjacent sections were used for the following analyses.
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7

Immunolocalization of NigA2 in A. niger

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The A. niger N402 wild type cells were harvested from solid MM, covered with a porous cellophane membrane, embedded in optimal cutting temperature compound (OCT; Tissue Tek, Sakura Finetek Europe B.V., Alphen aan den Rijn, The Netherlands) and frozen in a cryostat Leica CM3000, (Leica Microsystems GmbH, Wetzlar, Germany) at −30 °C and cut into 10 µm-thick cryosections. The sections were fixed with 2% paraformaldehyde for 20 min at 22 °C. After washing with PBS (pH 7.4) at 22 °C the cells were blocked with 1 % BSA in PBS. The sections were incubated with anti-mouse NigA2 antibodies (1:1000 in 1% BSA in PBS) [34 (link)] for 2 h at 37 °C and then washed with PBS. After washing, the sections were incubated overnight with secondary goat anti-mouse-Alexa-488 antibodies (1:400) (Molecular Probes, Thermo Fisher Scientific Inc., Waltham, MA, USA) in 1% BSA in PBS, at 4 °C. The next day, the sections were washed with PBS and mounted in Vectashield for nuclear staining with 4′,6-diamidino-2-phenylindole (DAPI). Immunostained embedded cryoresin slides were observed with the inverted confocal microscope as described above.
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8

Brain Tissue Preparation Protocols

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Some brains were embedded in 4% low-melt agarose (LOW EEO, Laboratorios Conda S.A., Spain) in 0,1 M phosphate-buffered saline (PBS) and sectioned using a vibratome (Leica VT 1000S, Leica Microsystems GmbH, Germany) on the frontal, sagittal, horizontal or obliquehorizontal plane at 80 µm-thick. Other brains were cryoprotected with 30% sucrose in phosphate buffer (PB; 0.1M; pH 7.4) or with a solution of glycerol and DMSO in PB and were frozen with -60/-70°C isopentane (2-methyl butane, Sigma-Aldrich, Germany) (following the protocol of Rosene et al, 1986) (link). The frozen brains were preserved at -80°C until use. Frontal, horizontal or sagittal free-floating sections were obtained using a freezing sliding microtome (60 µm-thick, Microm HM 450, Thermo Fisher Scientific, United Kingdom) or a cryostat (40 µmthick, Leica CM 3000, Leica Microsystems GmbH). All sections were collected in 4°C PBS and then processed for in situ hybridization, immunohistochemistry or immunofluorescence.
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9

Cryosectioning and Zymography of Fetal Heads

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Fetal heads were embedded in OCT compound (Sakura Finetek Japan, Tokyo, Japan) immediately after dissection, frozen in liquid nitrogen, and stored at À808C until used. Serial sections (approximately 10 lm) were then cut at a cabinet temperature of À258C using a cryostat (Leica CM3000; Leica Microsystems, Wetzler, Germany) and dried in cold air for 5 minutes. The frozen sections were subjected to in situ zymography and immunohistochemical staining (Table 1).
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10

Immunohistochemical Analysis of Intestinal Tight Junctions

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The fixed jejunal samples were immersed in 30% sucrose in 50 mM PBS for two days at 4 °C, embedded in Tissue-Tek OCT compound (Sakura FineTechnical, Tokyo, Japan), and frozen on dry ice. Cryosections (thickness: 4 μm) were obtained using a cryostat (CM3000; Leica Microsystems, Wetzlar, Germany) and blocked with 2% normal goat serum (Vector Laboratories, Burlingame, CA, USA) for 30 min at 30 °C. Tissues were incubated in antibody retrieval buffer with 0.01 M citrate, pH 6.0, for 10 min at 90 °C, and then with primary antibodies against the TJ proteins claudin-1 (Cat#717800), claudin-2 (Cat#51600), claudin-7 (Cat#349100), and zonula occludens (ZO-1) (Cat#617300) [Thermo Fisher Scientific (Waltham, MA, USA)], claudin-3 (SAB4200607), and claudin-5 (SAB4200537) [Sigma-Aldrich (St. Louis, MO, USA)] at 4 °C overnight. After being washed with PBS, the fixed jejunal tissues were incubated with the secondary antibody Alexa-Fluor-488-conjugated goat anti-rabbit IgG (Thermo Fisher Scientific, Waltham, MA, USA) for 30 min at 30 °C. Nuclei were visualized in Vectashield Hardset Mounting medium with DAPI (Vector Laboratories, CA, USA). Imaging was performed using a confocal laser microscope, FluoViewTM FV1000 (Olympus, Tokyo, Japan), equipped with ×20 and ×40 objective lenses.
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