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161 protocols using axiocam hrm

1

Aggregates Degradation Dynamics Monitoring

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For determining degradation of Puromycin-induced p62 aggregates, HeLa cells treated with DMSO or 10 μM Ro-3306 for 24 h were incubated with 5 μg/ml Puromycin for the indicated time. Cells were fixed, immunostained with anti-p62 antibody, and observed with confocal microscopy (LSM 880 Meta plus Zeiss Axiovert Zoom; Zeiss) equipped with a 63×/1.40 oil-immersion objective lens (Plan-Apochromat; Zeiss) and a camera (AxioCam HRm; Zeiss) at RT.
For examining degradation of Htt97Q-GFP aggregates, HeLa cells stably expressing Tet-on Htt97Q-GFP were incubated with 1 μg/ml doxycycline for 10 h to induce Htt97Q-GFP expression. Cells were washed three times with PBS buffer and incubated with DMSO or 10 μM Ro-3306 for the indicated times. Htt97Q-GFP foci were observed with a confocal microscope (LSM 880 Meta plus Zeiss Axiovert Zoom; Zeiss) equipped with a 63×/1.40 oil-immersion objective lens (Plan-Apochromat; Zeiss) and a camera (AxioCam HRm; Zeiss) at RT.
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2

Indirect immunofluorescence analysis of VZV

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Indirect IFA was performed on cell spots of FACS sorted VZV or mock cultured NK cells (CD3CD56+). Cell spots were air dried on glass slides and fixed with 4% formaldehyde (Cytofix; BD Biosciences) at room temperature. Subsequently, cell spots were permeabilised with 0.1% Triton X-100 (Sigma-Aldrich) for 10 mins at room temperature. Cell spots were blocked with 20% donkey serum, and then stained against IE63 (1:500), pORF29 (1:750), or respective isotype control, for 1 hr at 37°C. Thereafter cell spots were stained with fluorochrome-conjugated secondary antibodies, and finally mounted with ProLong Gold Antifade Mountant with DAPI (Thermo Fisher Scientific). Imaging was performed with a ZEISS Axio Imager.M2 upright microscope with a ZEISS AxioCam HRm digital monochrome CCD camera for fluorescence imaging and ZEISS ApoTome.2 (Carl Zeiss Microscopy).
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3

Immunolabelling of Myoblasts for Apoptosis and Wnt Signaling

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For immunolabelling, iDUX4 myoblasts were fixed in 4% paraformaldehyde/PBS for 10 min, washed in 3 X PBS for 5 min and permeabilised for 5 min with 0.5% triton X100/PBS. Subsequently, cells were blocked for 1 h using 5% goat serum/PBS (blocking buffer). Primary antibodies were added in PBS and incubated overnight at 4°C. Primary antibodies were: rabbit polyclonal anti-Cleaved-CASPASE3 (Cell Signalling; 9661S; 1:400), mouse monoclonal anti-total β-CATENIN (BD; 610154; 1:200), rabbit monoclonal anti-Non phospho(Active)β-CATENIN (1:1000, 8814, Cell Signaling), chicken polyclonal anti-GFP (Abcam; ab13970; 1:1000), and mouse monoclonal anti-DUX4 (Millipore; 9A12; 1:1000). DUX4 antibody 9A12 recognises a region common to both DUX4 and DUX4c, so was also used to detect DUX4c expression as previously described (Bosnakovski et al., 2008a (link)). Cells were then washed in 3 x PBS for 5 min, secondary antibodies added in blocking buffer and incubated for 1 h at room temperature. Secondary antibodies were: AlexaFluor 594 goat anti-mouse (Invitrogen; A11005; 1:1000) and Alexa Fluor 488 goat anti-chicken IgY (H + L) (Invitrogen; A11039; 1:1000). Nuclei were counterstained with 0.3 μM DAPI in PBS for 10 min and mounted in PBS. Cells were imaged using a classic Zeiss Axiovert 200 M epifluorescence microscope with a Zeiss AxioCam HRm and AxioVision 4.4 software (Zeiss, Jena, Germany).
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4

Immunofluorescence Staining of Cell Adhesion Proteins

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Deparaffinized tissue sections or 4% paraformaldehyde-fixed HaCat cells were blocked with 10% goat serum and 5% bovine serum albumin (BSA) in PBS containing 0.5% Triton X-100 (PBST) for 20 min. Staining was performed using primary antibodies against FAK (1:100 dilution), fibronectin (1:100 dilution), Ly6g (1:100 dilution), or F4/80 (1:100 dilution) at 37 °C for 3 h. For staining of integrin α5 and β1 (1:100 dilution), sections were stained at 4 °C for overnight. The slides were subsequently incubated with the appropriate fluorescent-labeled secondary antibodies (1:500 dilution) at 37 °C for 1 h and then counterstained with Hoechst 33258 for 6 min. The slide was also stained F-actin by TRITC-phalloidin (25 μg/mL) at 37 °C for 1 h. The slides were then rinsed with PBST three times, mounted with FluorSave™ reagent (Calbiochem, La Jolla, CA, USA), and viewed with an epifluorescence microscope (Zeiss Axioplan 2 imaging; Zeiss, Oberkochen, Germany) equipped with a charge-coupled device camera (Zeiss AxioCam HRm, Zeiss) and quantification was performed using Axiovert software (Zeiss AxioVision Release 4.8.2, Zeiss).
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5

Immunolabelling of Myoblast Differentiation

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For immunolabelling, immortalized myoblasts were plated at 25 000 cells/well in 96 well plates and cultured for 48 h in proliferation medium, while primary myoblasts were cultured for 24 hours, before being switched to differentiation medium for 3 days. Cells were then fixed with 4% paraformaldehyde/PBS for 15 min, washed thrice with PBS, then permeabilised with 0.1% Triton/PBS for 10 min, washed thrice again with PBS then blocked in 10% goat serum (volume/volume percent) (DakoCytomation, Glostrup, Denmark) for 30 min before being incubated on a rocker overnight at 4oC with primary antibody against MyHC (MF-20, DSHB, IA, USA) at 1/400 in PBS supplemented with 1% goat serum
(v/v). Cells were then washed thrice with PBS before being incubated at room temperature for 30 min with AlexFluor conjugated secondary antibodies (eBioscience, Hertfordshire, UK) diluted 1:400 in PBS supplemented with 1% goat serum, washed thrice again with PBS and incubated at room temperature for 10 min in 1:1000 DAPI (4′, 6-diamidino-2-phenylindole)/PBS. Samples were imaged on a Zeiss Axiovert 200M microscope using a Zeiss AxioCam HRm and AxioVision software version 4.4 (Zeiss). At least three fields were taken at 100× magnification for each well, resulting in quantification of over 500 cells per well.
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6

Microscopic Imaging of M. smegmatis Cells

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Single snapshot micrographs of M. smegmatis cells were captured with a Zeiss Axioskop M, Zeiss Axio.Scope, and Zeiss Axio.Observer Z1. Briefly, 2.0–5.0 μl of liquid culture was placed between a No. 1.5 glass coverslip and microscope slide. A transmitted mercury lamp light was used together with filter cubes to visualize fluorescence using a ×100 1.4 NA plan apochromatic oil immersion objective lens. Samples were located using either transmitted light, differential interference contrast, or epifluorescence. Snapshot images were captured with either a Zeiss 1 MP or Zeiss AxioCam HRm monochrome camera. Images of the same experiment were captured with the same instrument and exposure settings. Green fluorescence of EGFP was detected using the Zeiss Filter Set 38 HE. Red fluorescence of mCherry was detected using the Zeiss Filter Set 43. Images were captured using AxioVision 4.7 or ZEN Blue Microscope and Imaging Software. Images were processed using Fiji (Schindelin et al., 2012 (link)); images of the same strain were contrasted to the same maximum and minimum within an experiment.
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7

Tissue Sectioning and Immunostaining

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Tissues were harvested, placed in optimal cutting temperature (OCT) mounting media (Tissue-Tek, Sakura Finetek, Torrance, CA, USA). Sectioned tissues were processed as previously described with anti-VV or Anti-Active Caspase-3. Tumor images were obtained with an Epson Perfection 2450 Photo Scanner (Epson, Toronto, ON, Canada), whereas magnifications were captured using a Zeiss AxioCam HRm inverted fluorescent microscope (Zeiss, Toronto, ON, Canada) and analyzed using AxioVision 4.0 software.
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8

Immunofluorescence Staining of Myogenic Cells

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Myofibres and myoblasts were fixed in 4% paraformaldehyde, permeabilised in 0.5% Triton-X (Sigma-Aldrich) for 10 min, washed with PBS then blocked for 30 min in 5% (v/v) swine and goat serum (DakoCytomation Glostrup, Denmark), incubated in primary antibodies overnight at 4°C [mouse anti-DUX4 antibody [9A12 mAb, a kind gift from Alexandra Belayew (University of Mons, Mons, Belgium), 1:2000], mouse anti-Pax7 antibody [AB528428, Developmental Studies Hybridoma Bank (DSHB); 1:20–1:100], mouse anti-MyoD antibody clone 5.8A (M3512, DakoCytomation; 1:50), mouse anti-myogenin antibody (F5D, DSHB; 1:15–1:50), mouse anti-MyHC antibody (MF20, DSHB; 1:400), rabbit anti-GFP antibody (A-11122, Thermo Fisher Scientific; 1:1000), rabbit anti-phospho-histone-H1 (06-597, Millipore, 1:300) and anti-phospho-histone-H3 antibodies (06-570, Millipore; 1:100). After washing, incubation for 1 h at room temperature with Alexa-Fluor-conjugated secondary antibodies (Thermo Fisher Scientific) (Moyle and Zammit, 2014 (link)).
Images were acquired on a Zeiss Axiovert 200 M microscope using a Zeiss AxioCamHRm and AxioVision version 4.4 (Zeiss) or a Zeiss Axioplan 2 with a Hamamatsu ORCA-ER camera with Openlab 3.1.7.
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9

Microfluidic Device Perfusion Visualization

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The device was connected to microtubing at the inlet and outlet, filled with sterile water, and sealed using the clamping system. The device was then connected to a micropump (PHD Ultra, Harvard Apparatus, Holliston, MA, USA) at the inlet, which was adjusted to pump a water solution colored with a trypan blue dye (Gibco, Fisher Scientific, Waltham, MA, USA) into the device at a controlled flow rate. The flow of the colored solution within the device was then monitored using live imaging microscopy (Zeiss AxioCam HRm, Carl Zeiss, Oberkochen, Germany). The flow of the colored solution was similarly observed through collagen hydrogels previously described, which were loaded into the compartments of the LN-on-a-chip.
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10

Immunofluorescent Staining of Macrophages and Signaling

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Deparaffinized tissue sections or 4% PFA-fixed BMDMs were blocked with 10% goat serum and 5% BSA in PBST for 20 min. Staining was performed using primary antibodies against F4/80 (1:100 dilution) at 37 °C for 3 h. For the staining of the αv integrin (1:100 dilution) or the phospho-NF-κB p65 (1:100 dilution), sections were stained at 4 °C overnight. The slides were subsequently incubated with the appropriate fluorescent-labeled secondary antibodies (1:500 dilution) at 37 °C for 1 h and were then counterstained with Hoechst 33258 for 6 min. The slide was viewed with an epifluorescence microscope (Zeiss Axioplan 2 imaging; Zeiss, Oberkochen, Germany) equipped with a charge-coupled device camera (Zeiss AxioCamHRm, Zeiss, Germany), and quantification was performed using Axiovert software (Zeiss AxioVision Release 4.8.2, Zeiss, Germany).
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