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6 protocols using las af tcs sp5

1

Neutrophil Depletion in SAH Mouse Model

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Wild type C57BL/6 mice were subjected to SAH and sham surgery with and
without neutrophil depletion and sacrificed at specific time points after
surgery. Brains were fixed in 4% paraformaldehyde for 24 h at
4°C after perfusion with PBS. They were cryoprotected in 30%
sucrose at 4 °C overnight and embedded in OCT solution and sectioned
into 40-μm cryosections. Free floating sections were incubated for 45
min in TBS containing 0.1% Triton X-100 and 5% normal goat serum
(NGS) and incubated with monoclonal antibody Ly6G (for neutrophils) or Iba-1
(Waka labs, 1:1,000 dilution)] overnight at 4 °C. Sections were
incubated in Alexa Fluor 488–goat anti-rabbit IgG (Invitrogen; 1:500
dilution) and Alexa Fluor 594–goat anti-mouse IgG (Invitrogen; 1:500
dilution) for 1 h at room temperature, rinsed, and air dried before mounting.
Confocal imaging was done using Leica DM 6000 CSF confocal microscope with Leica
Microsystems LAS AF-TCS SP5.
C57BL/6 EGFP-LysM (Lyz2tm1.1Graf) mice were
subjected to SAH and slices were evaluated 3 days after SAH using the same
preservation and staining technique with the exception that the staining was
performed in the dark to prevent loss of fluorescent signal. A secondary
anti-GFP antibody (ThermoFisher Scientific, Waltham, MA) was used to enhance the
signal. Confocal imaging was done using Leica DM 6000 CSF confocal microscope
with Leica Microsystems LAS AF-TCS SP5.
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2

NHERF1 and VEGFR2 Expression in Colorectal Cancer

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Frozen sections of colorectal cancer tissues (n = 10) and background normal tissues (n = 10) were selected from the tissue bank and cut at a thickness of 6 μm using a cryostat. The sections were fixed with 4% paraformaldehyde in PBS at room temperature for 30min. Sections were incubated for 30 min in 5% BSA blocking solution and probed with monoclonal mouse anti-human NHERF1 primary antibody (1:100) (BD Biosciences) and polyclonal rabbit anti-human VEGFR2 primary antibody (1:100) (Santa-Cruz). This study employed controls that omitted the primary and secondary antibodies. Following extensive washings, sections were incubated with an Alexa Fluor® 488-conjugated anti-mouse IgG (Life Technologies, Massachusetts, USA) at 1:200 dilution and Alexa Fluor® 594-conjugated anti-rabbit IgG (Life Technologies) at 1:200 dilution in the dark for 1 h. After washing three times to remove the unbound secondary antibody, cell nuclei were stained with Hoechst 33258 (Sigma). The sections were finally mounted with FluorSave™ (Calbiochem-Novabiochem Ltd., Nottingham, UK) and visualized with a confocal microscope (Leica Microsystems LAS AF-TCS SP5. Wetzlar, Germany).
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3

Measuring Intracellular Calcium Dynamics

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The intracellular Ca2+ concentration was measured using Fluo-3-AM (Molecular Probes). HEK293A cells seeded in a confocal dish were washed three times with PBS and incubated with 10 μM Fluo-3-AM for 30 min at 37 °C in 5% CO2. After proper rinsing, Ca2+ fluorescence (488 nm) was recorded by confocal microscopy. Images were captured every 10 s after Ang II or Hcy stimulation. The images were quantified by a Leica Microsystems laser scanning confocal microscope (LAS AF-TCS SP5).
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4

Subcellular Localization of NHERF1

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Cells were plated at a density of 1.0 × 105 per well into 6-well plates pre-placed with a glass coverslip. Following transfection, the cells on coverslips were treated with/without heparin and then washed three times with cold PBS. After fixed with 4% paraformaldehyde at room temperature for 30 min, the cells were permeabilized and blocked with a buffer containing 0.3% Triton X-100 and 5% bovine serum albumin for 30 min. To determine the subcellular localization of NHERF1, cells were probed with monoclonal mouse anti-human NHERF1 primary antibody (1:100) (BD Transduction Laboratories) and anti-Flag primary antibody (1:200) (Sigma-Aldrich, St. Louis, MO, USA). Following extensive wash for removing the primary antibodies, the cells were incubated with an Alexa Fluor® 488 donkey anti-mouse IgG (Life Technologies, MA, USA) at 1:200 dilution in the dark for 1 h. Prior to the examination under a fluorescent microscope, cell nuclei were stained with Hoechst 33258 (Sigma-Aldrich). Images were acquired with a confocal system (Leica Microsystems LAS AF-TCS SP5. Wetzlar, Germany). Control samples without adding primary or secondary antibodies were prepared for evaluating the non-specific staining in this study.
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5

Immunofluorescence and Alkaline Phosphatase Assays

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Immunofluorescence analysis was performed on 1% Matrigel-coated glass coverslip in wells or in situ in microfluidic channels with the same protocol. Cells were fixed in 4% formaldehyde (Sigma-Aldrich 78775) in PBS for 10 min at RT, washed in PBS, permeabilized for 1 h in PBS + 0.3% Triton X-100 (PBST) at RT, and blocked in PBST + 5% of HS (ThermoFisher 16050-122) for 5 h at RT. Cells were incubated overnight at 4 °C with primary antibodies (see Supplementary Table 2) in PBST + 3% of HS. After washing with PBS, cells were incubated with secondary antibodies (Alexa, Life Technologies) (Supplementary Table 2) for 45 min at RT. Nuclei were stained with either DAPI (4′,6-diamidino-2-phenylindole, Sigma-Aldrich F6057) or Hoechst 33342 (ThermoFisher 62249). In the case of Phalloidin staining (see Fig. 8f), Alexa Fluor 488 Phalloidin and Hoechst were added with secondary antibodies. Images were acquired with a Zeiss LSN700 or a Leica SP5 confocal microscope using ZEN 2012 or Leica TCS SP5 LAS AF (v2.7.3.9723) software, respectively.
For alkaline phosphatase staining, cells were fixed with a citrate–acetone–formaldehyde solution and stained using an alkaline phosphatase detection kit (Sigma-Aldrich 86R-1KT). Plates were scanned using an Epson scanner and scored manually.
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6

Visualization of Notochord Cell Dynamics

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Nomarski images were taken using a Nikon Eclipse (E800) microscope equipped with a 40× objective (NA 1.00) and a SPOT RtKE CCD camera (Diagnostic Instruments), and a Zeiss Imager.M2 microscope equipped with a 100× objective (NA 1.30) and a pco.sensicam camera (Pco Imaging). Confocal images were taken using a Leica TCS SP5 confocal laser-scanning microscope equipped with 40× oil-immersion and 63× water-immersion objectives (NA 1.25 and 1.40, respectively). If necessary, embryos were sedated using 0.2% MS222 (Sigma, A5040). To visualize the dynamics of F-actin (mCherry-UtrCH and lifeact-mEGFP) and myosin filaments (mCherry-MRLC), we collected z-stacks of notochord cells at regular intervals, as specified in the movie legends. ImageJ and Leica TCS SP5 LAS AF software package were used to perform maximum projections and to construct movies. Fluorescence intensity was measured with ImageJ. The kymograph was compiled using the kymograph plugin in ImageJ. The velocity of single actin filaments was determined by calculation from the kymograph and by manual tracking in time-lapse movies using the Manual Tracking plugin in ImageJ. Colocalization of actin and myosin was analyzed using the Intensity Correlation Analysis plugin in ImageJ.
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