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395 protocols using axiocam mrc

1

Imaging Embryonic Neural Development

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Whole embryo images were taken on Zeiss V20 Stereo microscope with an AxioCam MRc digital color camera (Carl Zeiss). Images of transverse section of neural tube were taken on AXIO Examiner Z1 compound microscope with an AxioCam MRc color camera (Carl Zeiss), or on a Leica SP5 confocal microscope (Leica). Confocal images, thickness 2.304 µm, were processed with ImageJ (Schneider et al., 2012) . Images were processed for figures using Adobe Photoshop (CC2017, Adobe) for size and resolution adjustment, and for figure preparation.
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2

Quantifying Intraepidermal Nerve Fibers

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A 3 mm punch skin biopsy was taken from the dorsum of the foot under 1% lidocaine local anaesthesia. Skin samples were immediately fixed in 4% (wt/vol.) paraformaldehyde for 24 h and then cryoprotected in sucrose for 18 h and cut into 50 μm thick sections. Immunohistochemistry was performed as previously described [9 (link)]. An image analysis camera AxioCam MRc (Ziess, Germany) and Leica QWin Standard V2.4 (Leica Microsystem Imaging, Cambridge, UK) were used to quantify intraepidermal nerve fibre density (IENFD), which is the total number of nerve fibres per millimeter length of epidermis (no./mm).
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3

Quantifying Epidermal Nerve Fiber Density

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A 3 mm punch skin biopsy was taken from the dorsum of the foot under 1% lidocaine local anesthesia. Skin samples were immediately fixed in 4% (wt./vol.) paraformaldehyde for 24 h and then cryoprotected in sucrose for 18 h and cut into 50 μm sections. Immunohistochemistry was performed as previously described.15 (link) An image analysis camera AxioCam MRc (Ziess, Germany) and Leica QWin Standard V2.4 (Leica Microsystems Imaging, Cambridge, United Kingdom) were used to quantify IENFD, which is the total number of nerve fibers per millimeter length of epidermis (No./mm).
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4

Isolation of Bone Marrow-Derived Mesenchymal Stem Cells

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To isolate cells resembling hMSCs, specimens were processed according to the protocol of Pittenger et al. [21 (link)], used for isolating bone marrow-derived MSCs with modifications for whole tissues. In brief, tumor specimens were washed twice in serum-free minimal essential medium–alpha (MEM-α, Mediatech, Herndon, VA), minced, dissociated, and passed through a series of cell strainers. Single cells were resuspended in standard “MSC Media,” consisting of MEM-α plus 10% certified fetal bovine serum (FBS; Lonza, Wlkersville, MA), 2 mM L-glutamine (50 U/ml, Mediatech), and penicillin/streptomycin (50 mg/ml, Flow Laboratories, Rockville, MD), and plated at a density of 2 × 106 live cells per 75 cm2 flask. After 24 hours, nonadherent cells were removed by two washes with phosphate-buffered saline (PBS; Mediatech), and adherent cells were cultured until they reached confluence. Cells were trypsinized (0.25% trypsin with 0.1% EDTA) and subcultured at a density of 5000 cells/cm2. These cells were cultured continuously through multiple passages. Cell cultures were observed with an inverted phase-contrast microscope (Axiovert 200; Zeiss, Hallbergmoos, Germany). Photographs of cells were taken with a digital camera (AxioCam MRc, Zeiss), using Xcap-Plus version 2.1 software (Epix Inc., Buffalo Grove, IL) at each passage.
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5

Microscopic Image Acquisition and Processing

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Images were acquired on an Axio Imager.A1 (Zeiss) microscope using either a 10x Zeiss EC Plan-NEOfluar or 20x Zeiss EC Plan-NEOfluar objective. Images were collected using AxioCam MRc (Zeiss). Raw images were visualized using AxiovisionRel. 4.7 (Zeiss) and processed using Image J.
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6

Histological Analysis of BAT, SAT, and Liver

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Tissues were fixed in 10% paraformaldehyde for inclusion in paraffin. BAT and SAT samples were cut and mounted in a section (3 μm) and stained (haematoxylin and eosin alcoholic (BioOptica) procedure)64 (link). Frozen sections of liver were cut (8 µm) with a cryostat and stained in filtered Oil Red O (10 min). Sections were washed in distilled water, counterstained with Mayer’s haematoxylin (3 min), mounted in aqueous mounting medium (glycerine jelly) and observed and photographed with a Zeiss AXIO microscope digitizing the images with a coupled camera (AxioCam MRC) and quantified with ImageJ software (RRID: SCR_003070).
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7

Visualizing SARS-CoV-2 Spike-Induced Cell Fusion

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HEK293T cells were seeded into 25 cm2 flasks (1 × 106 cells/flask) and were transfected with pINT2-(TK-EF1α-S-ΔRS-HA-TK) or pEGFP-C1 (mock control) using polyethyleneimine (PEI) transfection reagent (Polysciences, Inc.). S-ΔRS-HA ORF was chemically synthesized by Eurofins genomics (Milano, Italy) and integrated into a pINT2 transfer vector (1 (link)) to yield pINT2-(TK-EF1α-S-ΔRS-HA-TK). pEGFP-C1 was obtained from Clontech. HEK293T cells transfection was performed as previously described (23 (link)). For syncytia formation, HEK/ACE2/TMPRRS2/Puro cells were transiently cotransfected with pINT2-(TK-EF1α-S-ΔRS-HA-TK) and pEGFP-C1 plasmids at the same molar ratio (1:1), using PEI transfection reagent as described before. Twenty-four hours after co-transfection, syncytia were observed by inverted fluorescence microscopy (Zeiss-Axiovert-S100), and images were acquired by a digital camera (Zeiss-Axiocam-MRC).
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8

Analyzing DU145 Spheroid Morphology

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The volume, morphology, and integrity of DU145 spheroids were analyzed based on the methods reported by Friedrich et al. [25 (link)] and Vinci et al. [27 (link)]. After the initiation step, photomicrographs of the DU145 spheroids were recorded using the Axio Cam MRc image capture system (Carl Zeiss; Göttingen, Germany) coupled to an inverted Axio LabA1 microscope (Carl Zeiss) using the 10× objective, and analyzed with the aid of the AxioVision SE64 Rel. 4.9.1 software (Carl Zeiss). Then, the spheroids were treated with RPMI 1640 (NC), 1% DMSO (SC), 50 µM DTX (PC), or BrA (10–100 µM). For integrity/morphology analysis, a second photomicrograph of each spheroid was obtained after 72 h of treatment. The other photomicrographs were obtained every 48 h until 168 h. After each photomicrograph, 50% of the culture medium in each well was replaced along with the treatments. In the integrity/morphology assessment, each image was analyzed to detect irregular spheroids (without circular shape), cell disaggregation, or irregular cell agglomeration. For cell volume quantification, the circumferences of tumor spheroids were analyzed with the AxioVision SE Rel. 4.9.1 software using the “measure” tool, and the area was reported in μm3. All analyses were performed with six spheroids/replicates (n = 6) in three biological experiments (n = 3).
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9

Acridine Orange Direct Counting Method

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AODC was performed as described by Hobbie et al. (27 (link)). Briefly, samples were preincubated overnight in the dark with 0.025% yeast extract (Difco Laboratories, Detroit, MI) and 0.002% nalidixic acid (Sigma). After incubation, samples were fixed with 4% formaldehyde, serially diluted 10-fold, and stained for 2 min with acridine orange (Sigma) at a 0.1% (wt/vol) final concentration. Samples were filtered using polycarbonate filters (0.2-µm pore size and 25-mm diameter; Millipore) prestained with Irgalan black dye. Stained bacteria on the membrane filters were counted using an epifluorescence microscope (Axioskop 40; Carl Zeiss, Inc., Göttingen, Germany). Total direct bacterial counts (including viable and VBNC bacteria) were averaged after counting 20 microscopic fields. Photographic records of bacteria and biofilms were captured using a digital camera (AxioCam MRc; Carl Zeiss, Inc., Göttingen, Germany) connected to the epifluorescence microscope.
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10

In Situ Hybridization of Spot/vp and Spot/vpr-like Genes

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The fragments of Spot/vp (310bp) and Spot/vpr-like (288bp) sequences were cloned into pGEM-T easy vector (Promega, Madison, WI, USA). The linear DNAs, amplified by PCR, were used as templates for riboprobes construction using DIG-Oligonucleotide Labeling Kit (Roche Molecular Biochemicals, Mannheim, Germany). Cerebral ganglia, hepatopancreas and ovaries at early vitellogenic stage were dissected and prepared for the paraffin-cut section. The serial seven-micron sections were used for Hematoxylin-eosin (H&E) staining and in situ hybridisation [64 (link)], visualised by the BCIP/NBT Chromogen Kit (Solarbio, Beijing, China) and mounted in Clear-Mount. All sections were observed and photographed by fluorescence confocal microscope (version, Axio Imager A2) equipped with digital camera (version, AxioCam MRc) (Carl Zeiss, Jena, Germany). Three technical replicates were performed.
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